Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009117.1 Hibiscus syriacus cultivar Beakdansim tig00112604_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: 576650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:253896 original size:20 final size:20
Alignment explanation
Indices: 253873--253916 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
253863 TGAGTTATGT
*
253873 GTTGCGATTTACAAATTTGC
1 GTTGCGATTTACAAATTAGC
*
253893 GTTGCGATTTACAGATTAGC
1 GTTGCGATTTACAAATTAGC
253913 GTTG
1 GTTG
253917 TGAATTTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACAAATTAGC
Found at i:253922 original size:60 final size:60
Alignment explanation
Indices: 253731--253924 Score: 182
Period size: 60 Copynumber: 3.2 Consensus size: 60
253721 TTTGACTTTC
* * * * * *
253731 GCGTTGCGAATTTGACTT-TCGCGTTGCGAATTTGAC--TTTCGTGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTTAT-GTGTTGCG-ATTT-ACAAATTCGAGTTGCGAATTTCAATATA
* * *
253791 GCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGAGTTGTGAATTTCACTATC
1 GCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGAGTTGCGAATTTCAATATA
* * * *
253851 GCATTGCGAATTTGAGTTATGTGTTGCGATTTACAAATTTGCGTTGCG-ATTTACAGAT-TA
1 GCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGAGTTGCGAATTT-CA-ATATA
*
253911 GCGTTGTGAATTTG
1 GCGTTGCGAATTTG
253925 GAAAATCGCA
Statistics
Matches: 115, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
58 2 0.02
59 8 0.07
60 103 0.90
61 2 0.02
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.40
Consensus pattern (60 bp):
GCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGAGTTGCGAATTTCAATATA
Found at i:253940 original size:32 final size:32
Alignment explanation
Indices: 253903--253967 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
253893 GTTGCGATTT
**
253903 ACAGATTAGCGTTGTGAATTTGGAAAATCGCA
1 ACAGATTAGCGTTGCAAATTTGGAAAATCGCA
*
253935 ACAGATTCGCGTTGCAAATTTGGAAAATCGCA
1 ACAGATTAGCGTTGCAAATTTGGAAAATCGCA
253967 A
1 A
253968 TGCGATTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.26
Consensus pattern (32 bp):
ACAGATTAGCGTTGCAAATTTGGAAAATCGCA
Found at i:257448 original size:27 final size:27
Alignment explanation
Indices: 257418--257473 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
257408 GCGTTTTATA
*
257418 TAAAAATCTAGATGGCTTAGTTTTTTT
1 TAAAAATCCAGATGGCTTAGTTTTTTT
257445 TAAAAATCCAGATGGCTTAGTTTTTTT
1 TAAAAATCCAGATGGCTTAGTTTTTTT
257472 TA
1 TA
257474 CTAAAACTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.46
Consensus pattern (27 bp):
TAAAAATCCAGATGGCTTAGTTTTTTT
Found at i:258658 original size:17 final size:17
Alignment explanation
Indices: 258636--258700 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
258626 AGCCATCCCA
258636 CTGAGTCAACTCGCTGG
1 CTGAGTCAACTCGCTGG
** *
258653 CTGAGTTTACTCGTTGG
1 CTGAGTCAACTCGCTGG
* *
258670 CTGAGTTAACTCGTTGG
1 CTGAGTCAACTCGCTGG
* *
258687 CTAAGCCAACTCGC
1 CTGAGTCAACTCGC
258701 ATTGAGTGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (17 bp):
CTGAGTCAACTCGCTGG
Found at i:262330 original size:38 final size:35
Alignment explanation
Indices: 262252--262386 Score: 198
Period size: 35 Copynumber: 3.8 Consensus size: 35
262242 GATAATGTTG
* *
262252 AATATTCCTCTAGTATTGAATGTTGGCAATGACTC
1 AATATTCCACTAGTATTGAATGTTGGTAATGACTC
262287 AATATTCCACTAGTATTGAATGTTGGTGGTAATGACTC
1 AATATTCCACTAGTATTGAATG-T--TGGTAATGACTC
262325 AATATTCCACTAGTATTGAATGTTGGTAATGACTC
1 AATATTCCACTAGTATTGAATGTTGGTAATGACTC
* * *
262360 AATATCCCACTAGTATTGGATATTGGT
1 AATATTCCACTAGTATTGAATGTTGGT
262387 TATCCCACTA
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
35 57 0.62
36 1 0.01
37 1 0.01
38 33 0.36
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (35 bp):
AATATTCCACTAGTATTGAATGTTGGTAATGACTC
Found at i:262390 original size:25 final size:25
Alignment explanation
Indices: 262362--262446 Score: 143
Period size: 25 Copynumber: 3.4 Consensus size: 25
262352 AATGACTCAA
262362 TATCCCACTAGTATTGGATATTGGT
1 TATCCCACTAGTATTGGATATTGGT
*
262387 TATCCCACTACTATTGGATATTGGT
1 TATCCCACTAGTATTGGATATTGGT
*
262412 TATCCCACTAGTATTGGATGTTGGT
1 TATCCCACTAGTATTGGATATTGGT
*
262437 TATCTCACTA
1 TATCCCACTA
262447 TGTTTAATAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (25 bp):
TATCCCACTAGTATTGGATATTGGT
Found at i:268329 original size:22 final size:20
Alignment explanation
Indices: 268304--268343 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
268294 ATGTTTGTTT
268304 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
268326 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
268344 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:272130 original size:22 final size:20
Alignment explanation
Indices: 272105--272144 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
272095 ATGTTTGTTT
272105 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
272127 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
272145 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:273475 original size:35 final size:35
Alignment explanation
Indices: 273415--273528 Score: 176
Period size: 35 Copynumber: 3.3 Consensus size: 35
273405 ATTAGTTGGG
*
273415 GAATGTTGATAATG-CTCAATATTCCACTAGTATT
1 GAATGTTGGTAATGACTCAATATTCCACTAGTATT
273449 GAATGTTGGTAATGACTCAATATTCCACTAGTATT
1 GAATGTTGGTAATGACTCAATATTCCACTAGTATT
* *
273484 GAATGTTGGTAATGAATCAATATCCCACTAGTATT
1 GAATGTTGGTAATGACTCAATATTCCACTAGTATT
* *
273519 GGATATTGGT
1 GAATGTTGGT
273529 TATCCCACTA
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
34 13 0.18
35 61 0.82
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (35 bp):
GAATGTTGGTAATGACTCAATATTCCACTAGTATT
Found at i:273532 original size:25 final size:25
Alignment explanation
Indices: 273504--273563 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
273494 AATGAATCAA
273504 TATCCCACTAGTATTGGATATTGGT
1 TATCCCACTAGTATTGGATATTGGT
*
273529 TATCCCACTAGTATTGGATGTTGGT
1 TATCCCACTAGTATTGGATATTGGT
273554 TATCCCACTA
1 TATCCCACTA
273564 TGTTTAATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.38
Consensus pattern (25 bp):
TATCCCACTAGTATTGGATATTGGT
Found at i:274276 original size:21 final size:21
Alignment explanation
Indices: 274258--274300 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
274248 TCTGCTATAC
*
274258 CTGCAATAGCGCTCGCTATGA
1 CTGCAATAGCGCCCGCTATGA
274279 CTGCAATAGCGCCCGCTATGA
1 CTGCAATAGCGCCCGCTATGA
274300 C
1 C
274301 CGTAATCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (21 bp):
CTGCAATAGCGCCCGCTATGA
Found at i:277321 original size:12 final size:12
Alignment explanation
Indices: 277304--277328 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
277294 GTCAAATAAT
277304 TTAGGCACCAAA
1 TTAGGCACCAAA
277316 TTAGGCACCAAA
1 TTAGGCACCAAA
277328 T
1 T
277329 GGTGCTTTGT
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:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:283825 original size:14 final size:15
Alignment explanation
Indices: 283799--283828 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
283789 GTTGTTGTTG
283799 TGTTTTTTCTTTCTT
1 TGTTTTTTCTTTCTT
283814 TGTTTTTT-TTTCTT
1 TGTTTTTTCTTTCTT
283828 T
1 T
283829 TTCCGGTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (15 bp):
TGTTTTTTCTTTCTT
Found at i:284350 original size:3 final size:3
Alignment explanation
Indices: 284342--284422 Score: 144
Period size: 3 Copynumber: 26.7 Consensus size: 3
284332 AATGTATATT
*
284342 TAA TAA TAA TAA TAAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
284388 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
284423 TGGATAAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
3 72 0.96
4 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:285152 original size:114 final size:114
Alignment explanation
Indices: 284742--285380 Score: 1081
Period size: 114 Copynumber: 5.6 Consensus size: 114
284732 GAATTATGCC
* *
284742 AAAA-GTTGAACAAATTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
284806 TATGAACTTC--TCCGGAAAAGATAATCCATCAA-TTGATGGATTCAGGT
66 TATGAAC-TCGAACTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
284853 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**** * * * * * **
284918 TATGAACTTTCTCTGGAAAAGCTGATCCATTAA-ATGATGGATTCATAT
66 TATGAACTCGAACTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
284966 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
285031 TATGAACTCGAACTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACTCGAACTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
285080 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
285145 TATGAACTCGAACTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACTCGAACTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
285194 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
285259 TATGAACTCGAACTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACTCGAACTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
*
285308 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
285373 TATGAACT
66 TATGAACT
285381 TCTCTGGAAA
Statistics
Matches: 502, Mismatches: 22, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
111 5 0.01
112 65 0.13
113 121 0.24
114 311 0.62
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (114 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCGAACTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
Found at i:286318 original size:83 final size:83
Alignment explanation
Indices: 286146--286691 Score: 945
Period size: 83 Copynumber: 6.6 Consensus size: 83
286136 CCTACTGAAT
* * ** * *
286146 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTA-TGAACACATTCATCTTTTAGACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
* *
286210 ATGATT-GTTCTGTCCAAC
65 ATGATTGGTTTTGTCAAAC
* *
286228 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCACCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
*
286293 ATGATT-GTTCTGTCAAAC
65 ATGATTGGTTTTGTCAAAC
286311 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
286376 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
286394 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
286459 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
286477 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
286542 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
286560 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
286625 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
286643 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACAT
286692 ATCAAAGGTT
Statistics
Matches: 451, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
82 64 0.14
83 381 0.84
84 6 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
TGATTGGTTTTGTCAAAC
Found at i:287633 original size:1 final size:1
Alignment explanation
Indices: 287629--287695 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
287619 CCTTTTTCCC
* * * * * * * * *
287629 TTTTTTTTTTTCTTCTTTTTTTTTCTTTTTTTCTTTTCTCTTTTTTTCTTTTTTTTTCTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
287694 TT
1 TT
287696 CTTCAAGCAT
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:287647 original size:8 final size:8
Alignment explanation
Indices: 287628--287695 Score: 63
Period size: 7 Copynumber: 8.8 Consensus size: 8
287618 ACCTTTTTCC
287628 CTTTTTTT
1 CTTTTTTT
287636 -TTTTCTTCT
1 CTTTT-TT-T
*
287645 TTTTTTTT
1 CTTTTTTT
287653 CTTTTTTT
1 CTTTTTTT
*
287661 C-TTTTCT
1 CTTTTTTT
287668 CTTTTTTT
1 CTTTTTTT
287676 C-TTTTTT
1 CTTTTTTT
*
287683 -TTTCTTT
1 CTTTTTTT
287690 CTTTTT
1 CTTTTT
287696 CTTCAAGCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
7 21 0.43
8 21 0.43
9 3 0.06
10 4 0.08
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
CTTTTTTT
Found at i:287647 original size:10 final size:10
Alignment explanation
Indices: 287634--287699 Score: 61
Period size: 10 Copynumber: 7.0 Consensus size: 10
287624 TTCCCTTTTT
287634 TTTTTTCTTC
1 TTTTTTCTTC
*
287644 TTTTTTTTTC
1 TTTTTTCTTC
287654 -TTTTT-TTC
1 TTTTTTCTTC
*
287662 TTTTCTC-T-
1 TTTTTTCTTC
*
287670 TTTTTTCTTT
1 TTTTTTCTTC
287680 TTTTTTCTT-
1 TTTTTTCTTC
287689 TCTTTTTCTTC
1 T-TTTTTCTTC
287700 AAGCATAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
8 9 0.19
9 12 0.26
10 26 0.55
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:287647 original size:13 final size:13
Alignment explanation
Indices: 287631--287695 Score: 70
Period size: 12 Copynumber: 5.4 Consensus size: 13
287621 TTTTTCCCTT
287631 TTTTTTTTTCTTC
1 TTTTTTTTTCTTC
287644 TTTTTTTTTCTT-
1 TTTTTTTTTCTTC
287656 TTTTTCTTTTC-TC
1 TTTTT-TTTTCTTC
287669 --TTTTTTTCTT-
1 TTTTTTTTTCTTC
*
287679 TTTTTTTCT-TTC
1 TTTTTTTTTCTTC
287691 TTTTT
1 TTTTT
287696 CTTCAAGCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
10 5 0.11
11 6 0.13
12 17 0.38
13 17 0.38
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTCTTC
Found at i:287657 original size:23 final size:23
Alignment explanation
Indices: 287631--287695 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 23
287621 TTTTTCCCTT
287631 TTTTTTTTTCTTCTTTTTTTTTC
1 TTTTTTTTTCTTCTTTTTTTTTC
*
287654 TTTTTTTCTT-TTCTCTTTTTTTC
1 TTTTTTT-TTCTTCTTTTTTTTTC
287677 TTTTTTTTTCTTTCTTTTT
1 TTTTTTTTTC-TTCTTTTT
287696 CTTCAAGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 2 0.05
23 26 0.70
24 9 0.24
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (23 bp):
TTTTTTTTTCTTCTTTTTTTTTC
Found at i:287657 original size:33 final size:33
Alignment explanation
Indices: 287620--287689 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
287610 CTTGACCCAC
*
287620 CTTTTTCCCTTTT-TTTTTTTCTTCTTTTTTTTT
1 CTTTTTCCCTTTTCTCTTTTT-TTCTTTTTTTTT
**
287653 CTTTTTTTCTTTTCTCTTTTTTTCTTTTTTTTT
1 CTTTTTCCCTTTTCTCTTTTTTTCTTTTTTTTT
287686 CTTT
1 CTTT
287690 CTTTTTCTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (33 bp):
CTTTTTCCCTTTTCTCTTTTTTTCTTTTTTTTT
Found at i:299998 original size:15 final size:16
Alignment explanation
Indices: 299973--300005 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
299963 TTAGTTGTTG
299973 TTGTGTTTTTTCTTTC
1 TTGTGTTTTTTCTTTC
*
299989 TTGT-TTTTTTTTTTC
1 TTGTGTTTTTTCTTTC
300004 TT
1 TT
300006 TTTCCGGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (16 bp):
TTGTGTTTTTTCTTTC
Found at i:300531 original size:3 final size:3
Alignment explanation
Indices: 300523--300590 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
300513 AATGTATATT
300523 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
300571 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
300591 TGGATAAGAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:301619 original size:6 final size:6
Alignment explanation
Indices: 301605--301639 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
301595 CCTGGAAAAT
*
301605 GGGATA GGGAAA GGGAAA GGGAAA GGGAAA GGGAA
1 GGGAAA GGGAAA GGGAAA GGGAAA GGGAAA GGGAA
301640 GAGAAGGCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.51, T:0.03
Consensus pattern (6 bp):
GGGAAA
Found at i:301701 original size:19 final size:19
Alignment explanation
Indices: 301677--301713 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
301667 GTATTAATTT
*
301677 TTTAAAACATAATTTTTTC
1 TTTAAAAAATAATTTTTTC
*
301696 TTTAAAAAATACTTTTTT
1 TTTAAAAAATAATTTTTT
301714 ATTTTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAAAAAATAATTTTTTC
Found at i:306205 original size:22 final size:23
Alignment explanation
Indices: 306157--306206 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
306147 GGGGAATTAG
*
306157 TTCCCCTTCAAAGGAGGAATCGG
1 TTCCCCTTCAAAGGAGGAATCGA
*
306180 TTCCCCTTC-AA-GAGGGTATCGA
1 TTCCCCTTCAAAGGA-GGAATCGA
306202 TTCCC
1 TTCCC
306207 TCTGCCCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 13 0.54
23 9 0.38
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (23 bp):
TTCCCCTTCAAAGGAGGAATCGA
Found at i:320204 original size:19 final size:18
Alignment explanation
Indices: 320159--320207 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
320149 TCAACCTGAT
*
320159 TGACCCATTGACTTTGAC
1 TGACCCGTTGACTTTGAC
320177 TGACCCGTTGACTTTGATC
1 TGACCCGTTGACTTTGA-C
*
320196 TGACTCGTTGAC
1 TGACCCGTTGAC
320208 CGTTAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (18 bp):
TGACCCGTTGACTTTGAC
Found at i:324205 original size:20 final size:22
Alignment explanation
Indices: 324169--324210 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
324159 TTTCATGGCT
324169 ATTGTTGTTTGGTTGTTTTTCG
1 ATTGTTGTTTGGTTGTTTTTCG
324191 ATTGTTG-TT-GTTGTTTTTCG
1 ATTGTTGTTTGGTTGTTTTTCG
324211 TCCACCCCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 2 0.10
22 7 0.35
ACGTcount: A:0.05, C:0.05, G:0.26, T:0.64
Consensus pattern (22 bp):
ATTGTTGTTTGGTTGTTTTTCG
Found at i:324618 original size:19 final size:19
Alignment explanation
Indices: 324572--324641 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
324562 TTGGACCTGA
324572 ATAAATAAATA-AGTAATAAT
1 ATAAATAAATACA--AATAAT
324592 A-AATATAACATACAAA-AAT
1 ATAA-ATAA-ATACAAATAAT
*
324611 ATAAATAAATATAAATAAT
1 ATAAATAAATACAAATAAT
*
324630 ATTAATATAATA
1 ATAAATA-AATA
324642 TATAATATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
18 6 0.14
19 19 0.45
20 13 0.31
21 3 0.07
22 1 0.02
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (19 bp):
ATAAATAAATACAAATAAT
Found at i:324636 original size:9 final size:9
Alignment explanation
Indices: 324572--324694 Score: 55
Period size: 10 Copynumber: 13.4 Consensus size: 9
324562 TTGGACCTGA
324572 ATAAATAA-
1 ATAAATAAT
*
324580 ATAAGTAAT
1 ATAAATAAT
*
324589 AATAAATATAAC
1 -AT-AA-ATAAT
*
324601 ATACAAAAAT
1 ATA-AATAAT
324611 ATAAATAAAT
1 ATAAAT-AAT
324621 ATAAATAAT
1 ATAAATAAT
324630 ATTAATATAAT
1 A-TAA-ATAAT
324641 AT--ATAAT
1 ATAAATAAT
324648 AT-AATGAA-
1 ATAAAT-AAT
*
324656 ATATATAACT
1 ATAAATAA-T
324666 ATATAAT-AT
1 ATA-AATAAT
*
324675 ATAAGT-AT
1 ATAAATAAT
324683 AT-AATAAT
1 ATAAATAAT
324691 ATAA
1 ATAA
324695 TATATATACG
Statistics
Matches: 89, Mismatches: 10, Indels: 31
0.68 0.08 0.24
Matches are distributed among these distances:
7 9 0.10
8 23 0.26
9 15 0.17
10 26 0.29
11 13 0.15
12 3 0.03
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
ATAAATAAT
Found at i:324658 original size:17 final size:17
Alignment explanation
Indices: 324587--324700 Score: 72
Period size: 15 Copynumber: 7.2 Consensus size: 17
324577 TAAATAAGTA
*
324587 ATAATA-AATATAACAT
1 ATAATATAATATAATAT
*
324603 ACAA-A-AATATAA-AT
1 ATAATATAATATAATAT
324617 A-AATATAA-ATAATAT
1 ATAATATAATATAATAT
324632 -TAATATAATAT-ATAAT
1 ATAATATAATATAAT-AT
*
324648 ATAATGAAATATATAACTAT
1 ATAAT-ATA-ATATAA-TAT
*
324668 ATAATAT-ATA-AGTAT
1 ATAATATAATATAATAT
324683 AT-A-ATAATATAATAT
1 ATAATATAATATAATAT
324698 ATA
1 ATA
324701 TACGTTTTCA
Statistics
Matches: 79, Mismatches: 5, Indels: 28
0.71 0.04 0.25
Matches are distributed among these distances:
13 4 0.05
14 12 0.15
15 32 0.41
16 8 0.10
17 7 0.09
18 2 0.03
19 5 0.06
20 8 0.10
21 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (17 bp):
ATAATATAATATAATAT
Found at i:324683 original size:23 final size:22
Alignment explanation
Indices: 324634--324700 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 22
324624 AATAATATTA
324634 ATATAATATATAATATAATGAAAT
1 ATATAATATATAATAT-AT-AAAT
*
324658 ATATAACTATATAATATATAAGT
1 ATATAA-TATATAATATATAAAT
324681 ATATAATAATATAATATATA
1 ATATAAT-ATATAATATATA
324701 TACGTTTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
22 1 0.03
23 21 0.52
24 8 0.20
25 10 0.25
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (22 bp):
ATATAATATATAATATATAAAT
Found at i:324684 original size:10 final size:9
Alignment explanation
Indices: 324608--324702 Score: 56
Period size: 9 Copynumber: 10.1 Consensus size: 9
324598 AACATACAAA
*
324608 AATATAAAT
1 AATATATAT
*
324617 AAATATAAAT
1 -AATATATAT
324627 AATAT-TA-
1 AATATATAT
324634 ATATAATATAT
1 A-AT-ATATAT
324645 AATATA-AT
1 AATATATAT
324653 GAA-ATATAT
1 -AATATATAT
324662 AACTATATAAT
1 AA-TATAT-AT
324673 ATATAAGTATAT
1 A-AT-A-TATAT
324685 AATA-ATAT
1 AATATATAT
324693 AATATATAT
1 AATATATAT
324702 A
1 A
324703 CGTTTTCAAA
Statistics
Matches: 71, Mismatches: 1, Indels: 27
0.72 0.01 0.27
Matches are distributed among these distances:
7 1 0.01
8 18 0.25
9 19 0.27
10 18 0.25
11 7 0.10
12 5 0.07
13 3 0.04
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (9 bp):
AATATATAT
Found at i:324699 original size:15 final size:15
Alignment explanation
Indices: 324614--324700 Score: 78
Period size: 15 Copynumber: 5.9 Consensus size: 15
324604 CAAAAATATA
324614 AATA-AATATA-AAT
1 AATATAATATATAAT
*
324627 AATATTA-ATATAAT
1 AATATAATATATAAT
324641 -ATATAATATAATGAA-
1 AATATAATAT-AT-AAT
324656 ATATATAACTATATAAT
1 A-ATATAA-TATATAAT
324673 -ATATAAGTATATAAT
1 AATATAA-TATATAAT
324688 AATATAATATATA
1 AATATAATATATA
324701 TACGTTTTCA
Statistics
Matches: 61, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
13 12 0.20
14 6 0.10
15 22 0.36
16 10 0.16
17 8 0.13
18 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (15 bp):
AATATAATATATAAT
Found at i:324738 original size:24 final size:22
Alignment explanation
Indices: 324694--324736 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
324684 TAATAATATA
*
324694 ATATATATACGTTTTCAAAACC
1 ATATATATACATTTTCAAAACC
324716 ATATATTATACATTTTCAAAA
1 ATATA-TATACATTTTCAAAA
324737 ACGTTTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATATATACATTTTCAAAACC
Found at i:324754 original size:70 final size:70
Alignment explanation
Indices: 324702--324948 Score: 361
Period size: 71 Copynumber: 3.5 Consensus size: 70
324692 TAATATATAT
* * *
324702 ACGTTTTCAAAACCATATATTATACATTTTCAAAAACGTTTTCAAAACTATATATTATGTATGTT
1 ACGTTTTCAAAACCATATATTATACGTTTTCAAAAA-GTTTTCAAAACTATATATTATATACGTT
324767 TTTAAA
65 TTTAAA
* *
324773 ATGTTTTCAAAACCATATGTTATACGTTTTCAAAAAGTTTTCAAAACTATATATTATATACGTTT
1 ACGTTTTCAAAACCATATATTATACGTTTTCAAAAAGTTTTCAAAACTATATATTATATACGTTT
324838 TTAAA
66 TTAAA
324843 ACGTTTTCAAAACCATATATTATACGTTTTCAAAAATGTTTTCAAAACTATATATTATATA-GTT
1 ACGTTTTCAAAACCATATATTATACGTTTTCAAAAA-GTTTTCAAAACTATATATTATATACGTT
324907 CTTTAAA
65 -TTTAAA
*** * * *
324914 ACGTTTTTTTAACTAGATATTATATGTTTTCAAAA
1 ACGTTTTCAAAACCATATATTATACGTTTTCAAAA
324949 CTATATATAT
Statistics
Matches: 161, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
70 69 0.43
71 92 0.57
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.43
Consensus pattern (70 bp):
ACGTTTTCAAAACCATATATTATACGTTTTCAAAAAGTTTTCAAAACTATATATTATATACGTTT
TTAAA
Found at i:324928 original size:36 final size:35
Alignment explanation
Indices: 324702--324949 Score: 252
Period size: 36 Copynumber: 7.1 Consensus size: 35
324692 TAATATATAT
* * *
324702 ACGTTTTCAAAACCATATATTATACA-TTTTCAAAA
1 ACGTTTTCAAAACTATATATTATATAGTTTT-TAAA
*
324737 ACGTTTTCAAAACTATATATTATGTATGTTTTTAAA
1 ACGTTTTCAAAACTATATATTATATA-GTTTTTAAA
* * * * *
324773 ATGTTTTCAAAACCATATGTTATA-CGTTTTCAAA
1 ACGTTTTCAAAACTATATATTATATAGTTTTTAAA
*
324807 AAGTTTTCAAAACTATATATTATATACGTTTTTAAA
1 ACGTTTTCAAAACTATATATTATATA-GTTTTTAAA
* * *
324843 ACGTTTTCAAAACCATATATTATA-CGTTTTCAAAA
1 ACGTTTTCAAAACTATATATTATATAGTTTT-TAAA
*
324878 ATGTTTTCAAAACTATATATTATATAGTTCTTTAAA
1 ACGTTTTCAAAACTATATATTATATAGTT-TTTAAA
*** * *
324914 ACGTTTTTTTAACTAGATATTATAT-GTTTTCAAA
1 ACGTTTTCAAAACTATATATTATATAGTTTTTAAA
324948 AC
1 AC
324950 TATATATATG
Statistics
Matches: 177, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
34 41 0.23
35 51 0.29
36 79 0.45
37 6 0.03
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.43
Consensus pattern (35 bp):
ACGTTTTCAAAACTATATATTATATAGTTTTTAAA
Found at i:326510 original size:19 final size:19
Alignment explanation
Indices: 326486--326531 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
326476 CACCATTTTT
* *
326486 TCCTCCCGTATCACCCTCC
1 TCCTCCCCTACCACCCTCC
326505 TCCTCCCCTACCACCCTCC
1 TCCTCCCCTACCACCCTCC
326524 TCCTCCCC
1 TCCTCCCC
326532 CTCCCCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.09, C:0.65, G:0.02, T:0.24
Consensus pattern (19 bp):
TCCTCCCCTACCACCCTCC
Found at i:326678 original size:16 final size:18
Alignment explanation
Indices: 326652--326695 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
326642 GGTAAGAAAT
326652 TTTTGTTTAAGT-TAG-TA
1 TTTT-TTTAAGTATAGATA
326669 TTTTTTTAAGTAGTAGATA
1 TTTTTTTAAGTA-TAGATA
326688 TTTTTTTA
1 TTTTTTTA
326696 TTATTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.29
17 4 0.17
18 3 0.12
19 10 0.42
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (18 bp):
TTTTTTTAAGTATAGATA
Found at i:326719 original size:17 final size:17
Alignment explanation
Indices: 326697--326752 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
326687 ATTTTTTTAT
326697 TATTATATTTATATAAA
1 TATTATATTTATATAAA
*
326714 TATTAT-TTTTTATTAAA
1 TATTATATTTATA-TAAA
* *
326731 -ATAATATTTATATAAT
1 TATTATATTTATATAAA
326747 TATTAT
1 TATTAT
326753 TTATTTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTATATTTATATAAA
Found at i:326725 original size:30 final size:31
Alignment explanation
Indices: 326689--326759 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 31
326679 TAGTAGATAT
*
326689 TTTTTTATT-ATTATATTTATATAAATATTA
1 TTTTTTATTAATAATATTTATATAAATATTA
*
326719 TTTTTTATTAAAATAATATTTATATAATTATTA
1 TTTTTTATT--AATAATATTTATATAAATATTA
326752 TTTATTTA
1 TTT-TTTA
326760 AATTTATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 9 0.26
33 22 0.63
34 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTTTATTAATAATATTTATATAAATATTA
Found at i:326768 original size:17 final size:16
Alignment explanation
Indices: 326698--326774 Score: 52
Period size: 17 Copynumber: 4.8 Consensus size: 16
326688 TTTTTTTATT
*
326698 ATTA-TATTTATATAA
1 ATTATTATTTATTTAA
*
326713 A-TATTATTTTTTATTAA
1 ATTATTA-TTTAT-TTAA
* * *
326730 AATAATATTTATAT-A
1 ATTATTATTTATTTAA
326745 ATTATTATTTATTTAA
1 ATTATTATTTATTTAA
*
326761 ATTTATTAATTATT
1 A-TTATTATTTATT
326775 ATTATTTGTG
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
14 2 0.04
15 15 0.32
16 7 0.15
17 19 0.40
18 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTATTATTTATTTAA
Found at i:326772 original size:24 final size:24
Alignment explanation
Indices: 326736--326781 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
326726 TTAAAATAAT
326736 ATTTATATAATTATTATTTATTTAA
1 ATTTATATAATTATTA-TTATTTAA
326761 ATTTAT-TAATTATTATTATTT
1 ATTTATATAATTATTATTATTT
326782 GTGCTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 9 0.43
25 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTTATATAATTATTATTATTTAA
Found at i:326779 original size:30 final size:30
Alignment explanation
Indices: 326714--326780 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
326704 TTTATATAAA
* *
326714 TATTATTTTTTATTAAAATAATATTTATAT
1 TATTATTATTTATTAAAATAATATTAATAT
* * *
326744 AATTATTATTTATTTAAAT-TTATTAATTAT
1 TATTATTATTTATTAAAATAATATTAA-TAT
326774 TATTATT
1 TATTATT
326781 TGTGCTAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TATTATTATTTATTAAAATAATATTAATAT
Found at i:328604 original size:21 final size:21
Alignment explanation
Indices: 328545--328604 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
328535 ATCTCCACAT
*
328545 GGTTACATTCCTAGCCAGCAA
1 GGTTACATTCCTAGCCCGCAA
* * *
328566 GGTTATATTCCTATCCCGCCA
1 GGTTACATTCCTAGCCCGCAA
*
328587 GGTTACATGCCTAGCCCG
1 GGTTACATTCCTAGCCCG
328605 TATGGTTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.27
Consensus pattern (21 bp):
GGTTACATTCCTAGCCCGCAA
Found at i:328611 original size:21 final size:21
Alignment explanation
Indices: 328542--328611 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
328532 GCTATCTCCA
*
328542 CATGGTTACATTCCTAGCCAG
1 CATGGTTACATTCCTAGCCCG
* * *
328563 CAAGGTTATATTCCTATCCCG
1 CATGGTTACATTCCTAGCCCG
*
328584 CCA-GGTTACATGCCTAGCCCG
1 -CATGGTTACATTCCTAGCCCG
*
328605 TATGGTT
1 CATGGTT
328612 TTATGAGACC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.03
21 36 0.92
22 2 0.05
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.30
Consensus pattern (21 bp):
CATGGTTACATTCCTAGCCCG
Found at i:330094 original size:139 final size:139
Alignment explanation
Indices: 329617--330253 Score: 915
Period size: 139 Copynumber: 4.6 Consensus size: 139
329607 ATGCATCTTC
* * * * * * * *
329617 GGGGACATGACTCATATAATA-GGAAATTATAACATATTCTCTGACATAATAATTGAAGGCACGC
1 GGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
* * * * *
329681 CCCTGGAAACGCGCTTTTACCACTTTGTTGCGTTCCCTCAAACATAATA-GTACTGACATAAATA
66 CCCCGGAAACGCGCTTTCACCACTTTATTGTGTCCCCTCAAACATAATAGGTACTGACATAAATA
329745 GTG-CCCCG
131 GTGCCCCCG
* * * *
329753 AGGGACATGAGTGACATAATAGAGCAATGATAACATATTTTATGACAAAATAATGGAAGGCGCGC
1 GGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
* *
329818 CCCCGGAAACGCGCTTTCACCACTTTGA-TGTGTCCCCTTAAACATAATAGGTACT-ATATAAAT
66 CCCCGGAAACGCGCTTTCACCACTTT-ATTGTGTCCCCTCAAACATAATAGGTACTGACATAAAT
**
329881 AGTGCATCCG
130 AGTGCCCCCG
* * *
329891 AGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAATAAAATAATGGAAGGCGCGC
1 GGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
** * *
329956 CCCTAGAAACGCGCTTTCACCACTTTATTGTGTCCCCTCAAACATAATAGGTACTGATATGAATA
66 CCCCGGAAACGCGCTTTCACCACTTTATTGTGTCCCCTCAAACATAATAGGTACTGACATAAATA
330021 GTGCCCCCG
131 GTGCCCCCG
330030 GGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
1 GGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
* * * *
330095 CCCCGGAAACGCGTTTTCACCACTTTGTTGTGTCCCCTCAAACATAATAGGTACTTACATGAATA
66 CCCCGGAAACGCGCTTTCACCACTTTATTGTGTCCCCTCAAACATAATAGGTACTGACATAAATA
330160 GTGCCCCCG
131 GTGCCCCCG
* *
330169 GGGGACATGAGTGACATAATAGGGTAATTATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
1 GGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
*
330234 CCCCGGAAACTCGCTTTCAC
66 CCCCGGAAACGCGCTTTCAC
330254 ATTAATAGTA
Statistics
Matches: 450, Mismatches: 45, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
136 17 0.04
137 89 0.20
138 118 0.26
139 226 0.50
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.25
Consensus pattern (139 bp):
GGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
CCCCGGAAACGCGCTTTCACCACTTTATTGTGTCCCCTCAAACATAATAGGTACTGACATAAATA
GTGCCCCCG
Found at i:330140 original size:277 final size:276
Alignment explanation
Indices: 329618--330253 Score: 952
Period size: 277 Copynumber: 2.3 Consensus size: 276
329608 TGCATCTTCG
* * * * * *
329618 GGGACATGACTCATATAATA-GGAAATTATAACATATTCTCTGACATAATAATTGAAGGCACGCC
1 GGGACATGAGTGACATAATAGGGAAATTATAACATATTCTCTGACAAAATAATGGAAGGCGCGCC
* * *
329682 CCTGGAAACGCGCTTTTACCACTTTGTTGCGTTCCCTCAAACATAATAGTACTGACATAAATAGT
66 CCTGGAAACGCGCTTTCACCACTTTATTGCGTCCCCTCAAACATAATAGTACTGACATAAATAGT
*
329747 GCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTTTATGACAAAATAATGGAAG
131 GCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTATGACAAAATAATGGAAG
* *
329812 GCGCGCCCCCGGAAACGCGCTTTCACCACTTTGATGTGTCCCCTTAAACATAATAGGTAC-TATA
196 GCGCGCCCCCGGAAACGCGCTTTCACCACTTTGATGTGTCCCCTCAAACATAATAGGTACTTACA
*
329876 TAAATAGTGCATCCGA
261 TAAATAGTGCACCCGA
* * * *
329892 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAATAAAATAATGGAAGGCGCGCC
1 GGGACATGAGTGACATAATAGGGAAATTATAACATATTCTCTGACAAAATAATGGAAGGCGCGCC
* * * *
329957 CCTAGAAACGCGCTTTCACCACTTTATTGTGTCCCCTCAAACATAATAGGTACTGATATGAATAG
66 CCTGGAAACGCGCTTTCACCACTTTATTGCGTCCCCTCAAACATAATA-GTACTGACATAAATAG
* * *
330022 TGCCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGA
130 TG-CCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTATGACAAAATAATGGA
* *
330087 AGGCGCGCCCCCGGAAACGCGTTTTCACCACTTTGTTGTGTCCCCTCAAACATAATAGGTACTTA
194 AGGCGCGCCCCCGGAAACGCGCTTTCACCACTTTGATGTGTCCCCTCAAACATAATAGGTACTTA
* * *
330152 CATGAATAGTGCCCCCGG
259 CATAAATAGTGCACCCGA
*
330170 GGGACATGAGTGACATAATAGGGTAATTATAACATATTCTCTGACAAAATAATGGAAGGCGCGCC
1 GGGACATGAGTGACATAATAGGGAAATTATAACATATTCTCTGACAAAATAATGGAAGGCGCGCC
* *
330235 CCCGGAAACTCGCTTTCAC
66 CCTGGAAACGCGCTTTCAC
330254 ATTAATAGTA
Statistics
Matches: 322, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
274 17 0.05
275 80 0.25
276 16 0.05
277 117 0.36
278 92 0.29
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (276 bp):
GGGACATGAGTGACATAATAGGGAAATTATAACATATTCTCTGACAAAATAATGGAAGGCGCGCC
CCTGGAAACGCGCTTTCACCACTTTATTGCGTCCCCTCAAACATAATAGTACTGACATAAATAGT
GCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTATGACAAAATAATGGAAG
GCGCGCCCCCGGAAACGCGCTTTCACCACTTTGATGTGTCCCCTCAAACATAATAGGTACTTACA
TAAATAGTGCACCCGA
Found at i:336833 original size:22 final size:23
Alignment explanation
Indices: 336795--336844 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
336785 TAAATATTTA
336795 AAAT-ATTTTATAGTTT-AAATCT
1 AAATAATTTTATAGTTTAAAAT-T
*
336817 AAATAATTTTAT-TTTTAAAATT
1 AAATAATTTTATAGTTTAAAATT
336839 AAATAA
1 AAATAA
336845 GACCTCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATAATTTTATAGTTTAAAATT
Found at i:337938 original size:32 final size:33
Alignment explanation
Indices: 337887--337962 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 33
337877 ATATATTATA
* * * **
337887 AAAATTTAA-AAATATTTTTATAATACTTTGAT
1 AAAATTTAATAAATATTTTTAGAACAATTCAAT
*
337919 AAAATTTAATAACTA-TTTTAGAACAATTCAAT
1 AAAATTTAATAAATATTTTTAGAACAATTCAAT
337951 AAAATTTAATAA
1 AAAATTTAATAA
337963 TTGTTTAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
32 33 0.89
33 4 0.11
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (33 bp):
AAAATTTAATAAATATTTTTAGAACAATTCAAT
Found at i:338466 original size:24 final size:24
Alignment explanation
Indices: 338434--338481 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
338424 TTGGTTAACA
338434 CATATGATAACTCTCCAAAAGAGT
1 CATATGATAACTCTCCAAAAGAGT
*
338458 CATATGATAACTTTCCAAAAGAGT
1 CATATGATAACTCTCCAAAAGAGT
338482 TATCTTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (24 bp):
CATATGATAACTCTCCAAAAGAGT
Found at i:343534 original size:12 final size:13
Alignment explanation
Indices: 343510--343548 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
343500 AACTATTTAT
343510 AAGAAATAAAAGA
1 AAGAAATAAAAGA
343523 AAGAAA-AAAAGA
1 AAGAAATAAAAGA
*
343535 AA-AACTAAAAGA
1 AAGAAATAAAAGA
343547 AA
1 AA
343549 ATAAAAGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 2 0.08
12 16 0.67
13 6 0.25
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (13 bp):
AAGAAATAAAAGA
Found at i:343549 original size:12 final size:11
Alignment explanation
Indices: 343513--343555 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
343503 TATTTATAAG
343513 AAATAAAAGAA
1 AAATAAAAGAA
*
343524 AGAAAAAAAGAA
1 A-AATAAAAGAA
343536 AAACTAAAAG-A
1 AAA-TAAAAGAA
343547 AAATAAAAG
1 AAATAAAAG
343556 TAGTAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 6 0.21
11 7 0.25
12 15 0.54
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (11 bp):
AAATAAAAGAA
Found at i:346266 original size:40 final size:40
Alignment explanation
Indices: 346211--346290 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
346201 CACCATTCGG
346211 ATAAAATGGGTAATAACAACATCTAAAGATAAAATGAAGT
1 ATAAAATGGGTAATAACAACATCTAAAGATAAAATGAAGT
346251 ATAAAATGGGTAATAACAACATCTAAAGATAAAATGAAGT
1 ATAAAATGGGTAATAACAACATCTAAAGATAAAATGAAGT
346291 TGTGTGATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.23
Consensus pattern (40 bp):
ATAAAATGGGTAATAACAACATCTAAAGATAAAATGAAGT
Found at i:347325 original size:31 final size:31
Alignment explanation
Indices: 347287--347358 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
347277 AACGTCCAAA
* * *
347287 TGACCAAAACTTAATAAAATAATAATATAAG
1 TGACCAAAACTCAATAAAAGAATAACATAAG
* *
347318 TGTCCAAAACTCAATAAAAGAATAACGTAAG
1 TGACCAAAACTCAATAAAAGAATAACATAAG
347349 TGACCAAAAC
1 TGACCAAAAC
347359 CTACATTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (31 bp):
TGACCAAAACTCAATAAAAGAATAACATAAG
Found at i:351266 original size:10 final size:10
Alignment explanation
Indices: 351245--351280 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
351235 ACTTATTTGA
351245 TTTTTCTCTCT
1 TTTTTCT-TCT
351256 TTTTTCTTCT
1 TTTTTCTTCT
*
351266 TTCTTCTTCT
1 TTTTTCTTCT
351276 TTTTT
1 TTTTT
351281 TTCACGTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:351551 original size:21 final size:21
Alignment explanation
Indices: 351527--351570 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
351517 TGAATGCTCT
*
351527 AAACAATATG-AACAACAATAC
1 AAACAAAATGTAACAA-AATAC
*
351548 AAACAAAATGTAATAAAATAC
1 AAACAAAATGTAACAAAATAC
351569 AA
1 AA
351571 CACCTATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.66, C:0.14, G:0.05, T:0.16
Consensus pattern (21 bp):
AAACAAAATGTAACAAAATAC
Found at i:351959 original size:17 final size:17
Alignment explanation
Indices: 351930--351962 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
351920 TAAAGAAAAT
351930 AAAACTAATAAAATAAC
1 AAAACTAATAAAATAAC
351947 AAAATCTAA-AAAATAA
1 AAAA-CTAATAAAATAA
351963 AAGAAGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAACTAATAAAATAAC
Found at i:373568 original size:18 final size:18
Alignment explanation
Indices: 373545--373619 Score: 84
Period size: 18 Copynumber: 4.1 Consensus size: 18
373535 GAGAATCTTT
373545 ATAGAAAA-AAAAGGAAAA
1 ATAGAAAAGAAAA-GAAAA
373563 ATAGAAAAGAAAA-AAGAA
1 ATAGAAAAGAAAAGAA-AA
373581 ATAGAAATAGAAAAGGAGAAA
1 ATAGAAA-AGAAAA-GA-AAA
373602 A-AGAAAAGAAAAGAAAA
1 ATAGAAAAGAAAAGAAAA
373619 A
1 A
373620 GAGGTGAAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.12
18 19 0.37
19 16 0.31
20 5 0.10
21 4 0.08
22 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (18 bp):
ATAGAAAAGAAAAGAAAA
Found at i:373576 original size:6 final size:6
Alignment explanation
Indices: 373552--373621 Score: 54
Period size: 6 Copynumber: 11.2 Consensus size: 6
373542 TTTATAGAAA
* * *
373552 AAAAAGG AAAAAT AGAAAAG AAAAAAG AAATAG AAATAG AAAAGGAG AAAAAG
1 AAAAA-G AAAAAG A-AAAAG -AAAAAG AAAAAG AAAAAG AAAA--AG AAAAAG
373605 -AAAAG -AAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG A
373622 GGTGAAACCA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
5 10 0.19
6 23 0.43
7 14 0.26
8 7 0.13
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:373588 original size:24 final size:25
Alignment explanation
Indices: 373566--373618 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
373556 AGGAAAAATA
373566 GAAAA-GA-AAAAAGAAATAGAAATA
1 GAAAAGGAGAAAAAGAAA-AGAAATA
373590 GAAAAGGAGAAAAAGAAAAGAAA-A
1 GAAAAGGAGAAAAAGAAAAGAAATA
373614 GAAAA
1 GAAAA
373619 AGAGGTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 11 0.41
25 7 0.26
26 9 0.33
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (25 bp):
GAAAAGGAGAAAAAGAAAAGAAATA
Found at i:373614 original size:19 final size:19
Alignment explanation
Indices: 373547--373614 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
373537 GAATCTTTAT
373547 AGAAAA-AAAAGGA-AAAA
1 AGAAAAGAAAAGGAGAAAA
* *
373564 TAGAAAAGAAAA-AAGAAAT
1 -AGAAAAGAAAAGGAGAAAA
373583 AGAAATAGAAAAGGAGAAAA
1 AGAAA-AGAAAAGGAGAAAA
373603 AGAAAAGAAAAG
1 AGAAAAGAAAAG
373615 AAAAAGAGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 12 0.29
19 20 0.48
20 10 0.24
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (19 bp):
AGAAAAGAAAAGGAGAAAA
Found at i:378279 original size:31 final size:31
Alignment explanation
Indices: 378244--378349 Score: 158
Period size: 31 Copynumber: 3.4 Consensus size: 31
378234 TTCAACGTTC
*
378244 AAGTGACCAAAACTTAATAAAATGATAACAT
1 AAGTGACCAAAACTTAATAAAACGATAACAT
* *
378275 AAGTGACCAAAACTTAATAAAACGATAGCGT
1 AAGTGACCAAAACTTAATAAAACGATAACAT
* *
378306 AAGTGATCAAAACTTAATAAAACAATAACAT
1 AAGTGACCAAAACTTAATAAAACGATAACAT
*
378337 AAGTGATCAAAAC
1 AAGTGACCAAAAC
378350 ATTTAATTTG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACGATAACAT
Found at i:383952 original size:37 final size:37
Alignment explanation
Indices: 383862--383962 Score: 121
Period size: 37 Copynumber: 2.7 Consensus size: 37
383852 TTCGTCCTAT
* * *
383862 TAAGATTCAAACTCTTAAAAATAGGATAAAATTTTAT
1 TAAGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
* * *
383899 TAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTAC
1 TAAGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
* * *
383936 TAAGATTTAAATTCCTAAAGATAGGAT
1 TAAGATTCAAACTCCTAAAAATAGGAT
383963 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (37 bp):
TAAGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
Found at i:384346 original size:18 final size:17
Alignment explanation
Indices: 384307--384349 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
384297 ATTATATAGA
384307 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
384323 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
384341 TATTATTAT
1 TATTATTAT
384350 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:384368 original size:58 final size:57
Alignment explanation
Indices: 384299--384423 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 57
384289 CCTTATTTAT
* * * *
384299 TATATAGATATT-TTA-TTCATTTATTTTTATTATTCATGTTATTATTATTATATGTATA
1 TATATATATATTATTATTTCATTTATTTTT-TTACT-ATATT-TTATTATTATATATATA
384357 TATATATATATTAAATTATTTTCATTTATTTTTTTACTATATTTTATTATTATATATATA
1 TATATATATATT--ATTA-TTTCATTTATTTTTTTACTATATTTTATTATTATATATATA
384417 TATATAT
1 TATATAT
384424 CTTTAATATT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
58 11 0.19
60 23 0.40
61 7 0.12
62 4 0.07
63 13 0.22
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (57 bp):
TATATATATATTATTATTTCATTTATTTTTTTACTATATTTTATTATTATATATATA
Found at i:384852 original size:2 final size:2
Alignment explanation
Indices: 384845--384874 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
384835 TAATACTTTG
*
384845 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
384875 TTTTTTCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:386482 original size:7 final size:7
Alignment explanation
Indices: 386472--386506 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
386462 ATTTATATTT
386472 TAATTCC
1 TAATTCC
386479 TAATTCC
1 TAATTCC
386486 TAATTCC
1 TAATTCC
386493 TAATTCC
1 TAATTCC
386500 TAATTCC
1 TAATTCC
386507 AACCAACCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATTCC
Found at i:386895 original size:35 final size:35
Alignment explanation
Indices: 386854--386929 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
386844 AATACAATCC
* *
386854 TCAATTATATTTTAAACCCCAAATTCTAAAGTAAT
1 TCAATTACATTTTAAACCCCAAATTCTAAAATAAT
* *
386889 TCAATTACATTTTAAATCCTAAATTCTAAAATAAT
1 TCAATTACATTTTAAACCCCAAATTCTAAAATAAT
*
386924 TTAATT
1 TCAATT
386930 TAGGGTTTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.41
Consensus pattern (35 bp):
TCAATTACATTTTAAACCCCAAATTCTAAAATAAT
Found at i:395362 original size:50 final size:50
Alignment explanation
Indices: 395287--395386 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
395277 GTCCACTACC
395287 TTAGCTATCCACACTAACGATTTTCCAACAAATTCACTAATTTGTTCTTT
1 TTAGCTATCCACACTAACGATTTTCCAACAAATTCACTAATTTGTTCTTT
395337 TTAGCTATCCACACTAACGATTTTCCAACAAATTCACTAATTTGTTCTTT
1 TTAGCTATCCACACTAACGATTTTCCAACAAATTCACTAATTTGTTCTTT
395387 CTTTTGAGGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.40
Consensus pattern (50 bp):
TTAGCTATCCACACTAACGATTTTCCAACAAATTCACTAATTTGTTCTTT
Found at i:395961 original size:64 final size:63
Alignment explanation
Indices: 395891--396070 Score: 168
Period size: 65 Copynumber: 2.8 Consensus size: 63
395881 TTGAACCCTT
* *
395891 AGTGCATCGGTGCA-CTAAGAGTGCATCGATGCATCAAGTGCATTCGGTG-TTTCA-AAATAGCC
1 AGTGCATCGGTGCAGCT--G-GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC
395953 AA
62 AA
* * * **
395955 AGTGCATCGATGCATGGCTGGTGCATTGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGGTGCA--GCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAA
* * * *
396020 AGTGCATCGGTGCATGGTAAGTGCATCGATGCATGAAATGAATTCGATGTT
1 AGTGCATCGGTGCA-GCT-GGTGCATCGATGCATCAAATGCATTCGATGTT
396071 CAATTTAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
64 41 0.43
65 50 0.52
66 3 0.03
67 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (63 bp):
AGTGCATCGGTGCAGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAA
Found at i:396044 original size:65 final size:65
Alignment explanation
Indices: 395910--396070 Score: 193
Period size: 65 Copynumber: 2.5 Consensus size: 65
395900 GTGCACTAAG
* *
395910 AGTGCATCGATGCATCAAGTGCATTCGGTG-TTTCAAAATAGCCAAAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAAAGTGCATCGATGCATGGCT
* * * ** *
395974 GGTGCATTGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCAAAGTGCATCGATGCATGGC
396037 T
65 T
* *
396038 AAGTGCATCGATGCATGAAATGAATTCGATGTT
1 -AGTGCATCGATGCATCAAATGCATTCGATGTT
396071 CAATTTAATT
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 27 0.33
65 52 0.63
66 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAAAGTGCATCGATGCATGGCT
Found at i:396109 original size:65 final size:63
Alignment explanation
Indices: 395911--396120 Score: 185
Period size: 65 Copynumber: 3.3 Consensus size: 63
395901 TGCACTAAGA
* * * * *
395911 GTGCATCGATGCATCAAGTGCATTCGGTGTTTCA-AAATAGC-CAAAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGAATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
395974 G
63 G
* * * **
395975 GTGCATTGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAA
1 GTGCATCGATGCATCAAATGAATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGTTG
* **
396040 GTGCATCGATGCATGAAATGAATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGAATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
396103 TG
62 TG
*
396105 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
396121 CTTTGATAAA
Statistics
Matches: 120, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 46 0.38
65 63 0.52
66 4 0.03
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGAATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:398839 original size:22 final size:22
Alignment explanation
Indices: 398767--398867 Score: 132
Period size: 22 Copynumber: 4.6 Consensus size: 22
398757 CATGACCCTG
*
398767 TGCATCGATGCACATTCAAGGCG
1 TGCATCGATGCACATTCAAGG-A
* * * *
398790 TGCATCGGTGTACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
*
398811 TGTATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
398833 TGCATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
398855 TGCATCGATGCAC
1 TGCATCGATGCAC
398868 TGTTAGGTGT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.24
22 34 0.51
23 17 0.25
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:404725 original size:65 final size:62
Alignment explanation
Indices: 404656--404836 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 62
404646 TTGAACCCTT
* * *
404656 AGTGCATTCGGTGCAATAAGAGTGCATCGATGCATCAAGTGCATTCGATGTTTC-AAAATAGTCA
1 AGTGCA-TCGGTGC-AT-GGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAATACTCA
* *
404720 GAGTGCATCGATGCATGGATGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCT
1 -AGTGCATCGGTGCATGGA--GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAAATACT
404785 CA
61 CA
*
404787 A-TGCATCGGTGCATGGTAAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGGTGCATGG--AGTGCATCGATGCATCAAATGCATTCGATGTT
404837 CAATTTAATT
Statistics
Matches: 102, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
62 2 0.02
63 2 0.02
64 36 0.35
65 52 0.51
66 1 0.01
67 9 0.09
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (62 bp):
AGTGCATCGGTGCATGGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAATACTCA
Found at i:404763 original size:64 final size:64
Alignment explanation
Indices: 404677--404886 Score: 239
Period size: 65 Copynumber: 3.2 Consensus size: 64
404667 TGCAATAAGA
* *
404677 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGTCAGAGTGCATCGATGCATGGATG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATACTCAGAGTGCATCGATGCATGGATG
* *
404741 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCA-A-TGCATCGGTGCATGG-
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTC--AAAATACTCAGAGTGCATCGATGCATGGA
*
404803 TAA
63 T-G
* ** * *
404806 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCAGGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ACTCAGAGTGCATCGATGCATGGA-T
404870 G
64 G
*
404871 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
404887 CTTTGATAAA
Statistics
Matches: 122, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
61 3 0.02
62 3 0.02
63 3 0.02
64 43 0.35
65 60 0.49
66 2 0.02
67 8 0.07
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATACTCAGAGTGCATCGATGCATGGATG
Found at i:413558 original size:36 final size:36
Alignment explanation
Indices: 413429--413541 Score: 183
Period size: 36 Copynumber: 3.1 Consensus size: 36
413419 AGTCTCAGTG
** *
413429 ATGTTGCTAAT-ATTGCTCAAGCTTCTAGTCCCAATT
1 ATGTTGCTAATGA-TGCTCAAGCCCCAAGTCCCAATT
413465 ATGTTGCTAATGATGCTCAAGCCCCAAGTCCCAATT
1 ATGTTGCTAATGATGCTCAAGCCCCAAGTCCCAATT
413501 ATGTTGCTAATGATGCTCAAGCCCCAAGTCCCAATT
1 ATGTTGCTAATGATGCTCAAGCCCCAAGTCCCAATT
413537 ATGTT
1 ATGTT
413542 TCCATTGTTG
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
36 72 0.99
37 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (36 bp):
ATGTTGCTAATGATGCTCAAGCCCCAAGTCCCAATT
Found at i:428965 original size:17 final size:17
Alignment explanation
Indices: 428901--428955 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
428891 TATCAAGTTA
428901 AATTATAATAAAAATAT
1 AATTATAATAAAAATAT
* *
428918 AAAAATACAAATAAAAATAT
1 --AATTA-TAATAAAAATAT
428938 AATTATAATAAAAATAT
1 AATTATAATAAAAATAT
428955 A
1 A
428956 TTTTATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 12 0.39
18 4 0.13
19 4 0.13
20 11 0.35
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AATTATAATAAAAATAT
Found at i:429419 original size:28 final size:30
Alignment explanation
Indices: 429350--429420 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 30
429340 GCAACCGCTC
*
429350 AGGGTCCT-TAATTTTTTGTATTTATAATT
1 AGGGTCCTCTAATTTTTTATATTTATAATT
*
429379 AGGGAT-C-CT-ATTTTTTATA-TTGTAATT
1 AGGG-TCCTCTAATTTTTTATATTTATAATT
429406 -GGGTCCTCTAATTTT
1 AGGGTCCTCTAATTTT
429421 ATAATTTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 9 0.26
28 14 0.40
29 6 0.17
30 1 0.03
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (30 bp):
AGGGTCCTCTAATTTTTTATATTTATAATT
Found at i:432934 original size:20 final size:20
Alignment explanation
Indices: 432905--432943 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
432895 TTTTCACCAC
*
432905 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
432925 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
432944 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:440884 original size:20 final size:20
Alignment explanation
Indices: 440855--440893 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
440845 TTTCCACCAC
*
440855 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
440875 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
440894 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:444408 original size:36 final size:36
Alignment explanation
Indices: 444368--444444 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
444358 AGTCTCAGTG
* ** *
444368 ATGTTGCTAAT-ATTGCTGAAGCTTCTAGTCCCAATT
1 ATGTTGCTAATGA-TGCTCAAGCCCCAAGTCCCAATT
444404 ATGTTGCTAATGATGCTCAAGCCCCAAGTCCCAATT
1 ATGTTGCTAATGATGCTCAAGCCCCAAGTCCCAATT
444440 ATGTT
1 ATGTT
444445 TCCATTGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 35 0.97
37 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (36 bp):
ATGTTGCTAATGATGCTCAAGCCCCAAGTCCCAATT
Found at i:446180 original size:2 final size:2
Alignment explanation
Indices: 446173--446198 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
446163 TGGAATTTAA
446173 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
446199 TTGTTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:448585 original size:38 final size:38
Alignment explanation
Indices: 448543--448620 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
448533 TGCTCTGCAT
448543 TGTTGCTTTTAACGTAGTTTGTGAAATAAATTTCATTA
1 TGTTGCTTTTAACGTAGTTTGTGAAATAAATTTCATTA
* *
448581 TGTTGTTTTTATCGTAGTTTGTGAAATAAATTTCATTA
1 TGTTGCTTTTAACGTAGTTTGTGAAATAAATTTCATTA
448619 TG
1 TG
448621 ACTTATTGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (38 bp):
TGTTGCTTTTAACGTAGTTTGTGAAATAAATTTCATTA
Found at i:449251 original size:312 final size:312
Alignment explanation
Indices: 448676--449289 Score: 1084
Period size: 312 Copynumber: 2.0 Consensus size: 312
448666 ACCCCTACAT
*
448676 TTTCACTTCAATCCCAACAGAACTTCTCTTTCTTTCCTTATTTCTCTGCTATAATTCTCACTTTC
1 TTTCACTTCAATCCCAACAAAACTTCTCTTTCTTTCCTTATTTCTCTGCTATAATTCTCACTTTC
448741 ATTTTATTTTATGGCGACCCATCTTGATTTTTCAAGTAAACTTTTTAGGTTTTTGTATTTCCCTC
66 ATTTTATTTTATGGCGACCCATCTTGATTTTTCAAGTAAACTTTTTAGGTTTTTGTATTTCCCTC
*
448806 AATTTTCCTTAATTTTTAAAAATAAATAATGTTTTTTCGAGCTTAATTTAACTACTCACTAGATG
131 AATTTTCCTTAATTTTTAAAAATAAATAATGTTTTTTCAAGCTTAATTTAACTACTCACTAGATG
* * * *
448871 TCATAATCTGAACTTAATTTCCTTTCTTGGGATGACTGGATCTTGAACATCTCAGCTGCTCAGTC
196 TCATAATCCGAACTTAATTTCCTCTCTTGGGATGACTAGATCTTCAACATCTCAGCTGCTCAGTC
* *
448936 TTAAACCAAACATTGGACGTTGCCGTTTCTCCTCCCCATCTTCCTTTCCTTA
261 TTAAACCAAACATTGGACCTTGCCATTTCTCCTCCCCATCTTCCTTTCCTTA
*
448988 TTTCTCTTCAATCCCAACAAAACTTCTCTTTCTTTCCTTATTTCTCTGCTATAATTCTCACTTTC
1 TTTCACTTCAATCCCAACAAAACTTCTCTTTCTTTCCTTATTTCTCTGCTATAATTCTCACTTTC
* * *
449053 ATTTTATTTTATGGCGCCCCATCTTGATTTTTCAGGTAAACTTTTTAGGTTTTTGTCTTTCCCTC
66 ATTTTATTTTATGGCGACCCATCTTGATTTTTCAAGTAAACTTTTTAGGTTTTTGTATTTCCCTC
449118 AATTTTCCTTAATTTTTAAAAATAAATAATGTTTTTTCAAGCTTAATTTAACTACTCACTAGATG
131 AATTTTCCTTAATTTTTAAAAATAAATAATGTTTTTTCAAGCTTAATTTAACTACTCACTAGATG
* *
449183 TCATAATCCGAACTTAATTTCCTCTCTTGGGCTGACTAGATCTTCAACATCTCAGCTGCTCGGTC
196 TCATAATCCGAACTTAATTTCCTCTCTTGGGATGACTAGATCTTCAACATCTCAGCTGCTCAGTC
* *
449248 TTAAACCAAACATTGGGCCTTGTCATTTCTCCTCCCCATCTT
261 TTAAACCAAACATTGGACCTTGCCATTTCTCCTCCCCATCTT
449290 AGTCCACAAA
Statistics
Matches: 286, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
312 286 1.00
ACGTcount: A:0.23, C:0.24, G:0.10, T:0.43
Consensus pattern (312 bp):
TTTCACTTCAATCCCAACAAAACTTCTCTTTCTTTCCTTATTTCTCTGCTATAATTCTCACTTTC
ATTTTATTTTATGGCGACCCATCTTGATTTTTCAAGTAAACTTTTTAGGTTTTTGTATTTCCCTC
AATTTTCCTTAATTTTTAAAAATAAATAATGTTTTTTCAAGCTTAATTTAACTACTCACTAGATG
TCATAATCCGAACTTAATTTCCTCTCTTGGGATGACTAGATCTTCAACATCTCAGCTGCTCAGTC
TTAAACCAAACATTGGACCTTGCCATTTCTCCTCCCCATCTTCCTTTCCTTA
Found at i:450271 original size:116 final size:112
Alignment explanation
Indices: 450046--450261 Score: 274
Period size: 116 Copynumber: 1.9 Consensus size: 112
450036 AGGGATCCTA
* * * *
450046 ATTTTAATCTAGGCAATTTTTATAATTTCATAAAAATTTTAGTTTTTATCCTCTTCTTTCATCTC
1 ATTTTAATCTAGGCAATTTTTATAATTTCATAAAAATTTTAATTTTGACCCTCTTCTTTCATCTA
* ** *
450111 TCTTATTAATTCATTCAATTTTTAATTAATTTTAACCAATTTTTTAT
66 TCTTATTAATTCAATCAATTTGGAATTAAATTTAACCAATTTTTTAT
*
450158 ATTTATAATCTAGGCACTAATTTTTATAATTTCAT-AAAATATTTAATTTTGACCCTCTTTTTTC
1 ATTT-TAATCTAGG--C-AATTTTTATAATTTCATAAAAAT-TTTAATTTTGACCCTCTTCTTTC
*
450222 ATTTATCTTACTT-ATTCAATCAATTTGGAATTAAATTTAA
61 ATCTATCTTA-TTAATTCAATCAATTTGGAATTAAATTTAA
450262 TCATGTTTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
112 4 0.05
113 9 0.10
115 6 0.07
116 67 0.76
117 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.52
Consensus pattern (112 bp):
ATTTTAATCTAGGCAATTTTTATAATTTCATAAAAATTTTAATTTTGACCCTCTTCTTTCATCTA
TCTTATTAATTCAATCAATTTGGAATTAAATTTAACCAATTTTTTAT
Found at i:451259 original size:10 final size:10
Alignment explanation
Indices: 451244--451286 Score: 68
Period size: 10 Copynumber: 4.3 Consensus size: 10
451234 TTCATCACAC
451244 CAAATCCTCT
1 CAAATCCTCT
451254 CAAATCCTCT
1 CAAATCCTCT
* *
451264 CAATTTCTCT
1 CAAATCCTCT
451274 CAAATCCTCT
1 CAAATCCTCT
451284 CAA
1 CAA
451287 CTTAAGGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:451331 original size:22 final size:23
Alignment explanation
Indices: 451301--451344 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
451291 AGGTATATTT
*
451301 TATTATATTTAA-TATTTATTAG
1 TATTATATTTAATTATTAATTAG
*
451323 TATTTTATTTAATTATTAATTA
1 TATTATATTTAATTATTAATTA
451345 TTTTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTATATTTAATTATTAATTAG
Found at i:453402 original size:6 final size:6
Alignment explanation
Indices: 453386--453436 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
453376 TATCTGCTCC
* ** * *
453386 TGACGA CGACGA TGACGA CAATGA TGACGA TGACGA TGACGA TGATGA
1 TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA
453434 TGA
1 TGA
453437 TGGTGATGAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (6 bp):
TGACGA
Found at i:453434 original size:3 final size:3
Alignment explanation
Indices: 453406--453451 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
453396 GATGACGACA
* * * *
453406 ATG ATG ACG ATG ACG ATG ACG ATG ATG ATG ATG GTG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
453452 CAATGAGGAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.07, G:0.35, T:0.26
Consensus pattern (3 bp):
ATG
Found at i:453457 original size:12 final size:12
Alignment explanation
Indices: 453386--453448 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
453376 TATCTGCTCC
* *
453386 TGACGACGACGA
1 TGACGATGATGA
**
453398 TGACGACAATGA
1 TGACGATGATGA
*
453410 TGACGATGACGA
1 TGACGATGATGA
453422 TGACGATGATGA
1 TGACGATGATGA
* *
453434 TGATGGTGATGA
1 TGACGATGATGA
453446 TGA
1 TGA
453449 TGACAATGAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (12 bp):
TGACGATGATGA
Found at i:453705 original size:35 final size:32
Alignment explanation
Indices: 453666--453750 Score: 89
Period size: 38 Copynumber: 2.4 Consensus size: 32
453656 TTTTGTTAAT
453666 TAATTTTGTTTATTACCATTTAATACCAGTTATTG
1 TAATTTTGTTTATTACCATTTAATA-C--TTATTG
*
453701 TAATTTTTTTATTATTTACCATTTAATACTTATTG
1 TAA-TTTTGT-TTA-TTACCATTTAATACTTATTG
*
453736 TAAGTTTGTTGTATT
1 TAATTTTGTT-TATT
453751 TAAAATTATA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
33 3 0.07
34 6 0.14
35 12 0.28
36 5 0.12
37 4 0.09
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.56
Consensus pattern (32 bp):
TAATTTTGTTTATTACCATTTAATACTTATTG
Found at i:458137 original size:2 final size:2
Alignment explanation
Indices: 458130--458204 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
458120 ATTAATTTGA
458130 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
458172 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
458205 CCCTCCTATT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:460860 original size:3 final size:3
Alignment explanation
Indices: 460852--460894 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
460842 ATTGGGTATA
* * *
460852 TTC TTC TTC TTC CTC TTC CTC TTC TTC CTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
460895 AGATGTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
TTC
Found at i:460876 original size:15 final size:15
Alignment explanation
Indices: 460856--460893 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
460846 GGTATATTCT
460856 TCTTCTTCCTCTTCC
1 TCTTCTTCCTCTTCC
*
460871 TCTTCTTCCTCTTCT
1 TCTTCTTCCTCTTCC
460886 TCTTCTTC
1 TCTTCTTC
460894 TAGATGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (15 bp):
TCTTCTTCCTCTTCC
Found at i:462390 original size:20 final size:20
Alignment explanation
Indices: 462365--462422 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
462355 AATACCTTTC
462365 AATTTAATAAAAAAATTAAA
1 AATTTAATAAAAAAATTAAA
* *
462385 AATTT-ATATTAAAAATTACA
1 AATTTAATA-AAAAAATTAAA
462405 AATTGTGAATAAATAAAA
1 AATT-T-AATAAA-AAAA
462423 AATTATTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.10
20 18 0.60
21 1 0.03
22 1 0.03
23 7 0.23
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (20 bp):
AATTTAATAAAAAAATTAAA
Found at i:463320 original size:61 final size:61
Alignment explanation
Indices: 463216--463333 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 61
463206 TGTACCAAGC
* * *
463216 TTACGCTCTAGTGTTAATCCGGATATAACACATAAGGTCGTGCCCACCACCTACACTAGGT
1 TTACACTCTAATGCTAATCCGGATATAACACATAAGGTCGTGCCCACCACCTACACTAGGT
* * * *
463277 TTACACTCTAATGCTAATTCGGATATGACACATAAGGTTGTGCCCTCCACCTACACT
1 TTACACTCTAATGCTAATCCGGATATAACACATAAGGTCGTGCCCACCACCTACACT
463334 TAGTGTCCTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (61 bp):
TTACACTCTAATGCTAATCCGGATATAACACATAAGGTCGTGCCCACCACCTACACTAGGT
Found at i:470375 original size:117 final size:119
Alignment explanation
Indices: 470209--470429 Score: 293
Period size: 117 Copynumber: 1.9 Consensus size: 119
470199 CCATTTATGG
* * *
470209 AAATTCTTTTTTGAGAAAATTACCACTTAGGTCCCTAAAATTTTGCCAATTTTATACTTCAACCA
1 AAATTCTTTTTTGAGAAAATTACCACTTAGGTACCTAAAAGTTTCCCAATTTTATACTTCAACCA
* * *
470274 CCATACTTTCAATATTTACATTTTGGTCACTAACTAAAACCATTTATGGAATAA
66 CCAAACTTTCAAAATTTACATTTTGGTCACTAACCAAAACCATTTATGGAATAA
* * * * ***
470328 AAATTC-TTTTTGAGAAAATT-CCACTTAGGTACTTAAACGTTTCCCAATTTTCTATTTTGGCCA
1 AAATTCTTTTTTGAGAAAATTACCACTTAGGTACCTAAAAGTTTCCCAATTTTATACTTCAACCA
**
470391 TGAAACTTTCAAAATTTACATTTTGGTCACTAACCAAAA
66 CCAAACTTTCAAAATTTACATTTTGGTCACTAACCAAAA
470430 TTTTGGGATA
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
117 67 0.77
118 14 0.16
119 6 0.07
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (119 bp):
AAATTCTTTTTTGAGAAAATTACCACTTAGGTACCTAAAAGTTTCCCAATTTTATACTTCAACCA
CCAAACTTTCAAAATTTACATTTTGGTCACTAACCAAAACCATTTATGGAATAA
Found at i:486239 original size:20 final size:20
Alignment explanation
Indices: 486214--486261 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
486204 GAGATCTAGA
486214 AGGAACTGGTTCAAATGGAG
1 AGGAACTGGTTCAAATGGAG
486234 AGGAACTGGTTCAAATGGAG
1 AGGAACTGGTTCAAATGGAG
486254 AGGAACTG
1 AGGAACTG
486262 CAAATGTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.10, G:0.35, T:0.19
Consensus pattern (20 bp):
AGGAACTGGTTCAAATGGAG
Found at i:487235 original size:18 final size:19
Alignment explanation
Indices: 487212--487254 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
487202 CAGTGATCCT
*
487212 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGATAATCTTAC
*
487230 ATTCCCACTGATAATCTTTC
1 ATT-CCACTGATAATCTTAC
487250 ATTCC
1 ATTCC
487255 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 14 0.67
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:489530 original size:30 final size:30
Alignment explanation
Indices: 489496--489651 Score: 113
Period size: 30 Copynumber: 5.3 Consensus size: 30
489486 ACTTAAAGAG
* *
489496 CTAAAATAGCAAAAATAGAAAATTAGAGGT
1 CTAAAATAGCAAAAACAGAAAATTAGAGGA
* ** *
489526 CTAAAATAGTAATTACAGAAACTTAGAGG-
1 CTAAAATAGCAAAAACAGAAAATTAGAGGA
** **
489555 CTAAACCAGCACAAAACAGAAACCTA-AGGA
1 CTAAAATAGCA-AAAACAGAAAATTAGAGGA
** * *
489585 CTAAAA-AGTGAAAATAGGAAAATAAG-GGA
1 CTAAAATAGCAAAAACA-GAAAATTAGAGGA
* * *
489614 CTACAATAGCAAAAACAGAAAGTTAAAGGA
1 CTAAAATAGCAAAAACAGAAAATTAGAGGA
489644 CTAAAATA
1 CTAAAATA
489652 AAATTTCACA
Statistics
Matches: 94, Mismatches: 26, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
28 5 0.05
29 32 0.34
30 57 0.61
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.16
Consensus pattern (30 bp):
CTAAAATAGCAAAAACAGAAAATTAGAGGA
Found at i:490022 original size:14 final size:14
Alignment explanation
Indices: 490003--490038 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
489993 CAAACTAGTG
490003 GCTTAAATATAAAT
1 GCTTAAATATAAAT
490017 GCTTAAATATAAAT
1 GCTTAAATATAAAT
*
490031 GCTGAAAT
1 GCTTAAAT
490039 GTAAGTGCTC
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:0.47, C:0.08, G:0.11, T:0.33
Consensus pattern (14 bp):
GCTTAAATATAAAT
Found at i:491314 original size:3 final size:3
Alignment explanation
Indices: 491306--491360 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
491296 AAATATAAAT
* *
491306 TAA TAA TAA TAA TAA TAA TGA -AA TAA TAA TAA TAA T-A TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
491352 TAC TAA TAA
1 TAA TAA TAA
491361 AAAGGCTCGG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
2 3 0.07
3 42 0.93
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:491320 original size:17 final size:15
Alignment explanation
Indices: 491306--491360 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 15
491296 AAATATAAAT
491306 TAATAATAATAATAA
1 TAATAATAATAATAA
*
491321 TAATGA-AATAATAA
1 TAATAATAATAATAA
491335 TAATAAT-ATAATAA
1 TAATAATAATAATAA
* *
491349 TATTACTAATAA
1 TAATAATAATAA
491361 AAAGGCTCGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
14 25 0.74
15 9 0.26
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (15 bp):
TAATAATAATAATAA
Found at i:491350 original size:20 final size:20
Alignment explanation
Indices: 491297--491360 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
491287 CAAAAATGTA
*
491297 AATATAA-ATTAATAATAAT
1 AATATAATAATAATAATAAT
491316 AATAATAATGAAATAATAATAAT
1 AAT-ATAAT--AATAATAATAAT
* *
491339 AATATAATAATATTACTAAT
1 AATATAATAATAATAATAAT
491359 AA
1 AA
491361 AAAGGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.08
20 16 0.42
22 5 0.13
23 14 0.37
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
AATATAATAATAATAATAAT
Found at i:491793 original size:134 final size:134
Alignment explanation
Indices: 491552--491905 Score: 489
Period size: 134 Copynumber: 2.6 Consensus size: 134
491542 GTCGTCTAAG
** * * *
491552 GGTGACACGGTTCCTACGTGATGAGGAAATCTGGTC-GAGGGATGACACTTCTCATACGTGATGA
1 GGTGACACGACTCCTACGTGATGAGG-AGTATGGTCAG-GGGATGACACTGCTCATACGTGATGA
* * *
491616 AGAGTTCTTGGTCATCTTTATGAAGGGTGATAACTCAGTTCCTACGCAATGAGGACTACTGGTTA
64 AGAGTTCTTGGACATCTTTAGGAAGGGTGATAACTCAGTTCCTACGCAATGAGGACGACTGGTTA
*
491681 TCTATA
129 TCTAGA
491687 GGTGACACGACTCCTACGTGATGAGGAGTATGGTCAGGGGATGACA-TGGCTCATACGTGATGAA
1 GGTGACACGACTCCTACGTGATGAGGAGTATGGTCAGGGGATGACACT-GCTCATACGTGATGAA
* * *
491751 GAGTTCTTGGACATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGGTTAT
65 GAGTTCTTGGACATCTTTAGGAAGGGTGATAACTCAGTTCCTACGCAATGAGGACGACTGGTTAT
*
491816 CTAGG
130 CTAGA
* * *
491821 GGTGACACGACTCCTAAGTGATGAAGAGATATGGTCAGGAGATGACACTGCTCATACGTGATGAA
1 GGTGACACGACTCCTACGTGATGAGGAG-TATGGTCAGGGGATGACACTGCTCATACGTGATGAA
* *
491886 GAGTT-ATGGCCATCTTTAGG
65 GAGTTCTTGGACATCTTTAGG
491906 GATAATGATT
Statistics
Matches: 197, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
133 1 0.01
134 132 0.67
135 63 0.32
136 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (134 bp):
GGTGACACGACTCCTACGTGATGAGGAGTATGGTCAGGGGATGACACTGCTCATACGTGATGAAG
AGTTCTTGGACATCTTTAGGAAGGGTGATAACTCAGTTCCTACGCAATGAGGACGACTGGTTATC
TAGA
Found at i:492227 original size:30 final size:30
Alignment explanation
Indices: 492193--492276 Score: 125
Period size: 30 Copynumber: 2.8 Consensus size: 30
492183 CAAAACTTTA
492193 TTTCAAAAGAAACAAACTCAAAGATT-TTGG
1 TTTCAAAAGAAAC-AACTCAAAGATTCTTGG
** *
492223 TTTCAAAAGAAATGACTCAAAGATTCTTTG
1 TTTCAAAAGAAACAACTCAAAGATTCTTGG
492253 TTTCAAAAGAAACAACTCAAAGAT
1 TTTCAAAAGAAACAACTCAAAGAT
492277 GATGGTTTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 11 0.23
30 37 0.77
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.27
Consensus pattern (30 bp):
TTTCAAAAGAAACAACTCAAAGATTCTTGG
Found at i:492807 original size:36 final size:35
Alignment explanation
Indices: 492676--492795 Score: 179
Period size: 36 Copynumber: 3.4 Consensus size: 35
492666 AGAAAAAAAA
*
492676 TGTCTCAAGCGAGACAAAATTTGTTTTGATAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AGAAAT
*
492712 TGTCTCAAGCGAAACAAAATTTGTTTTT-AGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
*
492746 TGTCTCAAGCGAGACAAAATTTGTTTTTAAAGTAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT-AAGAAAT
*
492782 TGTCTCAAGTGAGA
1 TGTCTCAAGCGAGA
492796 TCAACTTTGT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
34 33 0.43
36 44 0.57
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
Found at i:492921 original size:37 final size:38
Alignment explanation
Indices: 492823--492921 Score: 112
Period size: 37 Copynumber: 2.6 Consensus size: 38
492813 GAAATGAACT
* * * *
492823 CAAAATTTGTATCTCAAAGGGAAAATGTCTCAAGCGAGA
1 CAAAATTTGTATTTCAAA-AGAAACTGTCTCAAACGAGA
* * *
492862 CAAAATTTGT-TTTCGAATGAAACTGTCTCAAATGAGA
1 CAAAATTTGTATTTCAAAAGAAACTGTCTCAAACGAGA
492899 CAAAATTT-TATTTCAAAAGAAAC
1 CAAAATTTGTATTTCAAAAGAAAC
492922 AAAATCAAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
36 1 0.02
37 35 0.69
38 5 0.10
39 10 0.20
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.28
Consensus pattern (38 bp):
CAAAATTTGTATTTCAAAAGAAACTGTCTCAAACGAGA
Found at i:493045 original size:153 final size:153
Alignment explanation
Indices: 492844--493189 Score: 629
Period size: 153 Copynumber: 2.3 Consensus size: 153
492834 TCTCAAAGGG
* *
492844 AAAATGTCTCAAGCGAGACAAAATTTGTTTTCGAATGAAACTGTCTCAAATGAGACAAAATTTTA
1 AAAATATCTCAAGCGAGACAAAATTTGTTTTCGAATGAAACTATCTCAAATGAGACAAAATTTTA
*
492909 TTTCAAAAGAAACAAAATCAAAGATTTTCCAAAAGAAATTGTCTCAAGAGAGACAAAAATTTGTT
66 TTTCAAAAGAAACAAAATCAAAGATTTTCCAAAAGAAATTGTCTCAAGAGAGACAAAAAATTGTT
492974 TTAAACTTCTCAAAATTTGTGGA
131 TTAAACTTCTCAAAATTTGTGGA
*
492997 AAAATATCTCAAGCGAGACAGAATTTGTTTTCGAATGAAACTATCTCAAATGAGACAAAATTTTA
1 AAAATATCTCAAGCGAGACAAAATTTGTTTTCGAATGAAACTATCTCAAATGAGACAAAATTTTA
*
493062 TTTCAAAAGAAACAAAATCAATGATTTTCCAAAAGAAATTGTCTCAAGAGAGACAAAAAATTGTT
66 TTTCAAAAGAAACAAAATCAAAGATTTTCCAAAAGAAATTGTCTCAAGAGAGACAAAAAATTGTT
493127 TTAAACTTCTCAAAATTTGTGGA
131 TTAAACTTCTCAAAATTTGTGGA
* *
493150 AAAATATCTCAAGGGAGACATAATTTGTTTTCGAATGAAA
1 AAAATATCTCAAGCGAGACAAAATTTGTTTTCGAATGAAA
493190 AACGCCCTCA
Statistics
Matches: 186, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
153 186 1.00
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (153 bp):
AAAATATCTCAAGCGAGACAAAATTTGTTTTCGAATGAAACTATCTCAAATGAGACAAAATTTTA
TTTCAAAAGAAACAAAATCAAAGATTTTCCAAAAGAAATTGTCTCAAGAGAGACAAAAAATTGTT
TTAAACTTCTCAAAATTTGTGGA
Found at i:493074 original size:37 final size:37
Alignment explanation
Indices: 493001--493074 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
492991 TGTGGAAAAA
* * * *
493001 TATCTCAAGCGAGACAGAATTTGTTTTCGAATGAAAC
1 TATCTCAAACGAGACAAAATTTGTTTTCAAAAGAAAC
*
493038 TATCTCAAATGAGACAAAATTT-TATTTCAAAAGAAAC
1 TATCTCAAACGAGACAAAATTTGT-TTTCAAAAGAAAC
493075 AAAATCAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 1 0.03
37 30 0.97
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
TATCTCAAACGAGACAAAATTTGTTTTCAAAAGAAAC
Found at i:493481 original size:4 final size:4
Alignment explanation
Indices: 493472--493510 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
493462 TTTATGTATC
*
493472 ATGT ATGT ATGT ATAT ATGT ATGT ATGT AT-T GATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT -ATGT ATG
493511 ATTTTCTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 1 0.03
4 29 0.94
5 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:493493 original size:16 final size:16
Alignment explanation
Indices: 493472--493510 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
493462 TTTATGTATC
493472 ATGTATGTATGTATAT-
1 ATGTATGTATGTAT-TG
493488 ATGTATGTATGTATTG
1 ATGTATGTATGTATTG
493504 ATGTATG
1 ATGTATG
493511 ATTTTCTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (16 bp):
ATGTATGTATGTATTG
Found at i:498841 original size:29 final size:29
Alignment explanation
Indices: 498807--498876 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
498797 ACAGAAACCT
*
498807 AAGGACTAAAAAGTAAAAATAAGAAA-ATA
1 AAGGACTAAAAAGCAAAAAT-AGAAAGATA
* * *
498836 AGGGACTACAATAGCAAAAATAGAAAGTTA
1 AAGGACTA-AAAAGCAAAAATAGAAAGATA
498866 AAGGACTAAAA
1 AAGGACTAAAA
498877 TGAAATTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.61, C:0.07, G:0.17, T:0.14
Consensus pattern (29 bp):
AAGGACTAAAAAGCAAAAATAGAAAGATA
Found at i:498857 original size:30 final size:29
Alignment explanation
Indices: 498769--498875 Score: 78
Period size: 30 Copynumber: 3.6 Consensus size: 29
498759 TAGTAATTAC
*
498769 AGAAACTTAGAGG-CTAAACTAGCAAAAA-A
1 AGAAACATA-AGGACTAAA-TAGCAAAAATA
* * *
498798 CAGAAACCTAAGGACTAAAAAGTAAAAATA
1 -AGAAACATAAGGACTAAATAGCAAAAATA
498828 AGAAA-ATAAGGGACTACAATAGCAAAAAT-
1 AGAAACATAA-GGACTA-AATAGCAAAAATA
**
498857 AGAAAGTTAAAGGACTAAA
1 AGAAACAT-AAGGACTAAA
498876 ATGAAATTTC
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
28 3 0.05
29 28 0.44
30 31 0.48
31 2 0.03
ACGTcount: A:0.58, C:0.11, G:0.17, T:0.14
Consensus pattern (29 bp):
AGAAACATAAGGACTAAATAGCAAAAATA
Found at i:500264 original size:18 final size:18
Alignment explanation
Indices: 500238--500272 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
500228 CTTGAGTGGC
*
500238 GGCTGAGCTGGCGTTGGT
1 GGCTAAGCTGGCGTTGGT
*
500256 GGCTAAGCTGGTGTTGG
1 GGCTAAGCTGGCGTTGG
500273 CAGCTGATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.14, G:0.49, T:0.29
Consensus pattern (18 bp):
GGCTAAGCTGGCGTTGGT
Found at i:500537 original size:3 final size:3
Alignment explanation
Indices: 500518--500587 Score: 101
Period size: 3 Copynumber: 24.3 Consensus size: 3
500508 AATGTAAATG
*
500518 TAA TAT TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
500565 -AA TAA TAA CAA T-A TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
500588 TATTACTAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 6 0.10
3 54 0.90
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:504808 original size:6 final size:6
Alignment explanation
Indices: 504797--504844 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
504787 GGTATCAGAG
* * *
504797 TGTAGC TGTAGC TGTAGT TGTAGC TGTAGT TGTAGC TGTAGC CGTAGC
1 TGTAGC TGTAGC TGTAGC TGTAGC TGTAGC TGTAGC TGTAGC TGTAGC
504845 CCCACCTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.17, C:0.15, G:0.33, T:0.35
Consensus pattern (6 bp):
TGTAGC
Done.