Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 90 of 316
Found at i:27343837 original size:42 final size:42
Alignment explanation
Indices: 27343779--27343863 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
27343769 TATTTGGATA
*
27343779 TGGTTGGTCCACTTTTCTTGGATTTAATCTTGAATCATGATT
1 TGGTTGGTCCACTTTTCTTGGATTTAATCTTGAACCATGATT
27343821 TGGTTGGTCCACTTTTCTTGGATTTAATCTTGAACCATGATT
1 TGGTTGGTCCACTTTTCTTGGATTTAATCTTGAACCATGATT
27343863 T
1 T
27343864 CCTTTAATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (42 bp):
TGGTTGGTCCACTTTTCTTGGATTTAATCTTGAACCATGATT
Found at i:27348939 original size:21 final size:21
Alignment explanation
Indices: 27348914--27348953 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27348904 AGCATTCAAT
*
27348914 ATCATCATTCTCAATTCATGA
1 ATCATCATTCTAAATTCATGA
27348935 ATCATCATTCTAAATTCAT
1 ATCATCATTCTAAATTCAT
27348954 ATCTATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (21 bp):
ATCATCATTCTAAATTCATGA
Found at i:27351568 original size:12 final size:12
Alignment explanation
Indices: 27351552--27351584 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
27351542 AAAATCACAT
*
27351552 GAAAAAAAATGA
1 GAAAAAAAAAGA
27351564 -AAAAAAAAAGA
1 GAAAAAAAAAGA
27351575 GAAAAAAAAA
1 GAAAAAAAAA
27351585 AGCATAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (12 bp):
GAAAAAAAAAGA
Found at i:27351569 original size:13 final size:13
Alignment explanation
Indices: 27351553--27351586 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
27351543 AAATCACATG
*
27351553 AAAAAAAA-TGAA
1 AAAAAAAAGAGAA
27351565 AAAAAAAAGAGAA
1 AAAAAAAAGAGAA
27351578 AAAAAAAAG
1 AAAAAAAAG
27351587 CATAAGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (13 bp):
AAAAAAAAGAGAA
Found at i:27353160 original size:14 final size:14
Alignment explanation
Indices: 27353143--27353169 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27353133 CTACACACAT
27353143 ACATTTGCATACAC
1 ACATTTGCATACAC
27353157 ACATTTGCATACA
1 ACATTTGCATACA
27353170 AATTTTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (14 bp):
ACATTTGCATACAC
Found at i:27354769 original size:21 final size:21
Alignment explanation
Indices: 27354745--27354789 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
27354735 AAGAGTTATG
27354745 TTGAGCTAGTAGAGAGACTAA
1 TTGAGCTAGTAGAGAGACTAA
*
27354766 TTGAGCTAGTGGAGAGACTAA
1 TTGAGCTAGTAGAGAGACTAA
27354787 TTG
1 TTG
27354790 GATATGTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.27
Consensus pattern (21 bp):
TTGAGCTAGTAGAGAGACTAA
Found at i:27357358 original size:32 final size:32
Alignment explanation
Indices: 27357288--27357359 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
27357278 GGAGTGTGGC
* *
27357288 TGTGTGGGCCACATAGGTTAGGCCAAGTTAGG
1 TGTGTGGGCCACACAGGCTAGGCCAAGTTAGG
** *
27357320 CATGTGGGCCACACAGGCTAGGCCAAGTTGGG
1 TGTGTGGGCCACACAGGCTAGGCCAAGTTAGG
27357352 TGTGTGGG
1 TGTGTGGG
27357360 AGCACATGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.19, C:0.18, G:0.40, T:0.22
Consensus pattern (32 bp):
TGTGTGGGCCACACAGGCTAGGCCAAGTTAGG
Found at i:27360924 original size:12 final size:12
Alignment explanation
Indices: 27360907--27360931 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27360897 GGTGTTCATT
27360907 CGGTTAACCGAC
1 CGGTTAACCGAC
27360919 CGGTTAACCGAC
1 CGGTTAACCGAC
27360931 C
1 C
27360932 CGAAATAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:27361116 original size:9 final size:9
Alignment explanation
Indices: 27361102--27361171 Score: 95
Period size: 9 Copynumber: 7.8 Consensus size: 9
27361092 TAAGTATAAA
27361102 AATTAACCG
1 AATTAACCG
27361111 AATTAACCG
1 AATTAACCG
27361120 AATTAACCG
1 AATTAACCG
*
27361129 ATTTAACCG
1 AATTAACCG
* *
27361138 ATTTAAACG
1 AATTAACCG
* *
27361147 ATTTAACTG
1 AATTAACCG
27361156 AATTAACCG
1 AATTAACCG
27361165 AATTAAC
1 AATTAAC
27361172 AAAAAAAGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:27363898 original size:17 final size:18
Alignment explanation
Indices: 27363876--27363910 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
27363866 TAGAAGTTTG
27363876 TAAATTACAGC-AATAAA
1 TAAATTACAGCAAATAAA
27363893 TAAATTACAGCAAATAAA
1 TAAATTACAGCAAATAAA
27363911 AATATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (18 bp):
TAAATTACAGCAAATAAA
Found at i:27376542 original size:18 final size:18
Alignment explanation
Indices: 27376521--27376555 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27376511 ATCTTCAATT
27376521 TTTTTAAAATTTTTTTAA
1 TTTTTAAAATTTTTTTAA
**
27376539 TTTTTATGATTTTTTTA
1 TTTTTAAAATTTTTTTA
27376556 TTACAACTTG
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:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTTAAAATTTTTTTAA
Found at i:27380438 original size:22 final size:22
Alignment explanation
Indices: 27380398--27380453 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
27380388 AATAAAGTTG
*
27380398 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
27380418 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
27380440 TATTAATAATTTAT
1 AAATAATAAATTAT
27380454 TATAGGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:27381870 original size:13 final size:14
Alignment explanation
Indices: 27381854--27381887 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
27381844 AATTTATAAA
27381854 TTCTCTTTAAG-TT
1 TTCTCTTTAAGATT
*
27381867 TTCTTTTTAAGATT
1 TTCTCTTTAAGATT
27381881 TTCTCTT
1 TTCTCTT
27381888 GAATTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.65
Consensus pattern (14 bp):
TTCTCTTTAAGATT
Found at i:27384028 original size:45 final size:45
Alignment explanation
Indices: 27383962--27384058 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
27383952 ATACACCAAG
** * *
27383962 ATGAGTAAAACCATAGCTGAAAAATGTTATGACATCATGATAAAA
1 ATGAGTAAAACCATAAATGAAAAATGTTATGACATCAAGACAAAA
* *
27384007 ATGAGTAAAATCC-TAAATGAAAGATGTTATGACATCAAGACGAAA
1 ATGAGTAAAA-CCATAAATGAAAAATGTTATGACATCAAGACAAAA
27384052 ATGAGTA
1 ATGAGTA
27384059 TGACTATGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 43 0.96
46 2 0.04
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (45 bp):
ATGAGTAAAACCATAAATGAAAAATGTTATGACATCAAGACAAAA
Found at i:27393693 original size:19 final size:20
Alignment explanation
Indices: 27393665--27393710 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
27393655 ATTTTTCAAT
*
27393665 AAATTATTTACATTTTT-TA
1 AAATTTTTTACATTTTTATA
* *
27393684 TAATTTTTTATATTTTTATA
1 AAATTTTTTACATTTTTATA
27393704 AAATTTT
1 AAATTTT
27393711 AAATACTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
AAATTTTTTACATTTTTATA
Found at i:27400560 original size:9 final size:9
Alignment explanation
Indices: 27400546--27400650 Score: 63
Period size: 9 Copynumber: 11.2 Consensus size: 9
27400536 TCATTTCTAT
27400546 TTTTAATAA
1 TTTTAATAA
27400555 TTTTAATAA
1 TTTTAATAA
27400564 CTTTT-ATAA
1 -TTTTAATAA
27400573 TTTTAAAATAA
1 TTTT--AATAA
* *
27400584 TTCTTTTATAT
1 -T-TTTAATAA
*
27400595 TTTTAATAT
1 TTTTAATAA
*
27400604 TTTTTATAA
1 TTTTAATAA
*
27400613 TATTT--TAG
1 T-TTTAATAA
* *
27400621 TTTTTATCTA
1 TTTTAAT-AA
27400631 TTTTAATAA
1 TTTTAATAA
27400640 TTTTAATAA
1 TTTTAATAA
27400649 TT
1 TT
27400651 ATGTATATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
7 3 0.04
8 7 0.09
9 41 0.54
10 14 0.18
11 7 0.09
12 1 0.01
13 3 0.04
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (9 bp):
TTTTAATAA
Found at i:27400602 original size:20 final size:20
Alignment explanation
Indices: 27400555--27400611 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
27400545 TTTTTAATAA
27400555 TTTTAATAA--CTTTTATAAT
1 TTTTAATAATTCTTTTAT-AT
*
27400574 TTTAAAATAATTCTTTTATAT
1 TTT-TAATAATTCTTTTATAT
27400595 TTTTAAT-ATT-TTTTATA
1 TTTTAATAATTCTTTTATA
27400612 ATATTTTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 7 0.21
19 6 0.18
20 8 0.24
21 5 0.15
22 7 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTAATAATTCTTTTATAT
Found at i:27401181 original size:19 final size:19
Alignment explanation
Indices: 27401141--27401181 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
27401131 CAACGTGAAC
*
27401141 AAATAATTTAAAAACTATA
1 AAATAATTTAAAAACTAAA
* *
27401160 AAATATTTTAAAAATTAAA
1 AAATAATTTAAAAACTAAA
27401179 AAA
1 AAA
27401182 ACATAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATAATTTAAAAACTAAA
Found at i:27401352 original size:33 final size:33
Alignment explanation
Indices: 27401311--27401377 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
27401301 TGATGGCGAA
27401311 TTCGACTCCTTTTAAAAGATTGTGAGTTAAATT
1 TTCGACTCCTTTTAAAAGATTGTGAGTTAAATT
27401344 TTCGACTCCTTTTAAAAGATTGTGAGTTAAATT
1 TTCGACTCCTTTTAAAAGATTGTGAGTTAAATT
27401377 T
1 T
27401378 ATCTTAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (33 bp):
TTCGACTCCTTTTAAAAGATTGTGAGTTAAATT
Found at i:27401502 original size:18 final size:16
Alignment explanation
Indices: 27401471--27401536 Score: 73
Period size: 16 Copynumber: 4.1 Consensus size: 16
27401461 AATTTATTAC
27401471 ATTTTTTAAAATTTTA
1 ATTTTTTAAAATTTTA
27401487 ATTTTTTGAAACATTTTA
1 ATTTTTT-AAA-ATTTTA
*
27401505 GGTTTTTT--AATTTTA
1 -ATTTTTTAAAATTTTA
*
27401520 ATTTTTAAAAATTTTA
1 ATTTTTTAAAATTTTA
27401536 A
1 A
27401537 AATTAAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
14 5 0.12
15 6 0.14
16 16 0.38
17 3 0.07
18 6 0.14
19 6 0.14
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.59
Consensus pattern (16 bp):
ATTTTTTAAAATTTTA
Found at i:27401542 original size:6 final size:6
Alignment explanation
Indices: 27401533--27401557 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27401523 TTTAAAAATT
27401533 TTAAAA TTAAAA TTAAAA TTAAAA T
1 TTAAAA TTAAAA TTAAAA TTAAAA T
27401558 GACACAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TTAAAA
Found at i:27406509 original size:24 final size:23
Alignment explanation
Indices: 27406477--27406524 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
27406467 AAAAAAGTAA
27406477 GCCCATTTTTTGGGTCGAGTTAG
1 GCCCATTTTTTGGGTCGAGTTAG
27406500 GCCCATTTTTTGGGTCGAGTTAG
1 GCCCATTTTTTGGGTCGAGTTAG
27406523 GC
1 GC
27406525 TCGAGTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.19, G:0.31, T:0.38
Consensus pattern (23 bp):
GCCCATTTTTTGGGTCGAGTTAG
Found at i:27407492 original size:13 final size:13
Alignment explanation
Indices: 27407474--27407498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27407464 CTTAAAAAAA
27407474 TAAAAAATAAATC
1 TAAAAAATAAATC
27407487 TAAAAAATAAAT
1 TAAAAAATAAAT
27407499 ATTTTTATAA
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:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAAATAAATC
Found at i:27408174 original size:42 final size:41
Alignment explanation
Indices: 27408127--27408267 Score: 140
Period size: 42 Copynumber: 3.4 Consensus size: 41
27408117 TGCATCATGT
* ** *
27408127 ATCATCAGATAAACTAAAGCAAACATACTGACATGTAGGTGC
1 ATCATCAGATATACCGAAGAAAACATACTGACATGTA-GTGC
* * * *
27408169 ATCATCTGATGTACCGAAGAAAACATATTGGCATGTAAGTGC
1 ATCATCAGATATACCGAAGAAAACATACTGACATGT-AGTGC
*
27408211 ATCATTAGATATACCGAAGAAAACATACTAGCACATG-AGTGC
1 ATCATCAGATATACCGAAGAAAACATACT-G-ACATGTAGTGC
* *
27408253 ATAATCAGACATACC
1 ATCATCAGATATACC
27408268 AAAACAATAA
Statistics
Matches: 80, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
42 74 0.93
43 2 0.03
44 4 0.05
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (41 bp):
ATCATCAGATATACCGAAGAAAACATACTGACATGTAGTGC
Found at i:27409793 original size:43 final size:43
Alignment explanation
Indices: 27409696--27409815 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 43
27409686 ACCGAGATTT
* * *
27409696 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTGTTGA
1 GATTACATGTAAGACCATGTCTGGGACAGTGGCATCGTATTGA
*
27409739 GATTACGTGTAAGACTC-TGTCTGGGACAGTGGCATCG-ATATGTA
1 GATTACATGTAAGAC-CATGTCTGGGACAGTGGCATCGTAT-TG-A
* * * *
27409783 -TTTACATGTAAGATCATATCTGGGATA-TGGCAT
1 GATTACATGTAAGACCATGTCTGGGACAGTGGCAT
27409816 TGTACGAGCT
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
42 8 0.12
43 54 0.84
44 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.33
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACAGTGGCATCGTATTGA
Found at i:27410245 original size:42 final size:42
Alignment explanation
Indices: 27410136--27410269 Score: 153
Period size: 42 Copynumber: 3.2 Consensus size: 42
27410126 TGCTTTTCTT
* * * * *
27410136 AAAAACACTGCTAAAGAA-TATGACCTTTAGTGGCGCTTTCTCC
1 AAAAACGCCGCTAAAGAACT-TGACTTTTAGCGACGCTTTC-CC
* * * *
27410179 ACAAACGCCACTAAAGAACCTGACTTTTAGCGTCGCTTTCCC
1 AAAAACGCCGCTAAAGAACTTGACTTTTAGCGACGCTTTCCC
*
27410221 AAAAATGCCGCTAAAGAACTTGACTTTTAGCGACGCTTTCCC
1 AAAAACGCCGCTAAAGAACTTGACTTTTAGCGACGCTTTCCC
27410263 AAAAACG
1 AAAAACG
27410270 GCACTAGAAG
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
42 45 0.59
43 31 0.41
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACTTGACTTTTAGCGACGCTTTCCC
Found at i:27410991 original size:23 final size:23
Alignment explanation
Indices: 27410946--27411688 Score: 527
Period size: 23 Copynumber: 32.6 Consensus size: 23
27410936 ACATAAACTA
*
27410946 AATTT-CAGCAAC-TAAACAATTC
1 AATTTGCAGC-ACTTAAACACTTC
* *
27410968 AATTTGCAGTACTTAAAAACTTC
1 AATTTGCAGCACTTAAACACTTC
* * *
27410991 AATTTACAACATTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
*
27411014 AATTTGCAGCACTTTAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* * * *
27411037 AATTTACAACATTTAAACACTTT
1 AATTTGCAGCACTTAAACACTTC
*
27411060 AATTTGCAGCACTTTAACA-TCTC
1 AATTTGCAGCACTTAAACACT-TC
** * * * * *
27411083 AATTAACAACATTTATACTCCTC
1 AATTTGCAGCACTTAAACACTTC
* * *
27411106 AA-TTACAGCGA-TAAAACATTTC
1 AATTTGCAGC-ACTTAAACACTTC
27411128 AATTT-CTAGCAAC-TAAACACTTC
1 AATTTGC-AGC-ACTTAAACACTTC
* * *
27411151 AATTTACAACATTTAAACAC-TC
1 AATTTGCAGCACTTAAACACTTC
* * *
27411173 AATTTACATCA-TTTAACACTTC
1 AATTTGCAGCACTTAAACACTTC
*
27411195 AATTTGCAGCACTTTAACA-TCTC
1 AATTTGCAGCACTTAAACACT-TC
** * * * *
27411218 AATTAACAACATTTATACACCTC
1 AATTTGCAGCACTTAAACACTTC
* *
27411241 AA-TTACAGCGA-TAAAACA-TCTC
1 AATTTGCAGC-ACTTAAACACT-TC
*
27411263 AATTTCCAGCAAC-TAAACACTTC
1 AATTTGCAGC-ACTTAAACACTTC
*
27411286 AATTTGCAGTACTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* * *
27411309 AATTTACAACATTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* *
27411332 AATTTACAGCATTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
*
27411355 AATTTGCAGCACTTTAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* *
27411378 AATTTACAGCATTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* *
27411401 AATTTGCAGCACTTTAACATTTC
1 AATTTGCAGCACTTAAACACTTC
** * * * *
27411424 AATTAACAACAATTATACACCTC
1 AATTTGCAGCACTTAAACACTTC
*
27411447 AA-TTACAG-A-TATAAA-ACATCTC
1 AATTTGCAGCACT-TAAACAC-T-TC
*
27411469 AATTTCCAGCAAC-TAAACACTTC
1 AATTTGCAGC-ACTTAAACACTTC
*
27411492 AATTTGCAGTACTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* * * * *
27411515 AATTTACAACATTTAAGCACTTT
1 AATTTGCAGCACTTAAACACTTC
* * *
27411538 AATTTACAACATTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
** *
27411561 AATTTATAGCA-TTTAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* *
27411583 AACTTGCAGCACTTTAACACTTC
1 AATTTGCAGCACTTAAACACTTC
** *
27411606 AATTTATAGCATTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
*
27411629 AATTTGCAGCACTTTAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* *
27411652 AATTTACAGCATTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
*
27411675 AATTTGCTGCACTT
1 AATTTGCAGCACTT
27411689 TCATACCTTC
Statistics
Matches: 569, Mismatches: 122, Indels: 59
0.76 0.16 0.08
Matches are distributed among these distances:
20 3 0.01
21 11 0.02
22 91 0.16
23 454 0.80
24 7 0.01
25 3 0.01
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (23 bp):
AATTTGCAGCACTTAAACACTTC
Found at i:27411224 original size:135 final size:137
Alignment explanation
Indices: 27411004--27411347 Score: 561
Period size: 135 Copynumber: 2.5 Consensus size: 137
27410994 TTACAACATT
*
27411004 TAAACACTTCAATTTGCAGCACTTT-AACACTTCAATTTACAACATTTAAACACTTTAATTTGCA
1 TAAACACTTCAATTTGCAGCA-TTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTGCA
* *
27411068 GCACTTTAACATCTCAATTAACAACATTTATACTCCTCAATTACAGCGATAAAACATTTCAATTT
65 GCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTT
*
27411133 CTAGCAAC
130 CCAGCAAC
* * *
27411141 TAAACACTTCAATTTACAACATTTAAACAC-TCAATTTACATCATTT-AACACTTCAATTTGCAG
1 TAAACACTTCAATTTGCAGCATTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTGCAG
27411204 CACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTC
66 CACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTC
27411269 CAGCAAC
131 CAGCAAC
* * *
27411276 TAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTACAG
1 TAAACACTTCAATTTGCAGCATTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTGCAG
27411341 CA-TTTAA
66 CACTTTAA
27411348 ACACTTCAAT
Statistics
Matches: 191, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
135 111 0.58
136 38 0.20
137 42 0.22
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (137 bp):
TAAACACTTCAATTTGCAGCATTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTGCAG
CACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTC
CAGCAAC
Found at i:27411464 original size:137 final size:138
Alignment explanation
Indices: 27410960--27411689 Score: 529
Period size: 137 Copynumber: 5.3 Consensus size: 138
27410950 TCAGCAACTA
* * * * * * * ** *
27410960 AACAATTCAATTTGCAGTACTTAAAAACTTCAATTTACAACA-TTTAAACACTTCAATTTGCAGC
1 AACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAACACTTCAATTAACAAC
* * * * * * *
27411024 ACTTTAACACTTCAATTTACAACATTTAAACACTTTAATTTGCAGCACTTT-AACA-TCTCAATT
66 A-ATTAACACCTCAACTTACAGCACTTAAACACTTCAATTTACAGCA-TTTAAACACT-TCAATT
** *
27411087 AACAACA-TTT
128 TGCAGCACTTT
* * * * *
27411097 ATACTCCTCAA-TTACAGCGA-TAAAACATTTCAATTT-CTAGCAAC--TAAACACTTCAATTTA
1 A-ACACTTCAATTTACAGC-ATTTAAACACTTCAATTTGC-AGC-ACTTTAAACACTTCAATTAA
* * * * *
27411157 CAACATTTAA-ACACTCAATTTACATCA-TTTAACACTTCAATTTGCAGCACTTT-AACA-TCTC
62 CAACAATTAACAC-CTCAACTTACAGCACTTAAACACTTCAATTTACAGCA-TTTAAACACT-TC
** *
27411218 AATTAACAACA-TTT
124 AATTTGCAGCACTTT
* * * **
27411232 ATACACCTCAA-TTACAGCGA-TAAAACA-TCTCAATTTCCAGCAAC--TAAACACTTCAATTTG
1 A-ACACTTCAATTTACAGC-ATTTAAACACT-TCAATTTGCAGC-ACTTTAAACACTTCAATTAA
** * * * * *
27411292 CAGTACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTACAGCATTTAAACACTTCAA
62 CAACAATT-AACACCTCAACTTACAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTCAA
27411357 TTTGCAGCACTTT
126 TTTGCAGCACTTT
*
27411370 AACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTT-AACATTTCAATTAACAAC
1 AACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAACACTTCAATTAACAAC
* **
27411434 AATTATACACCTCAA-TTACAG-A-TATAAA-ACATCTCAATTTCCAGCAACTAAACACTTCAAT
66 AATTA-ACACCTCAACTTACAGCACT-TAAACAC-T-TCAATTTACAGCATTTAAACACTTCAAT
* *
27411495 TTGCAGTACTTA
127 TTGCAGCACTTT
* * * * * * * *
27411507 AACACTTCAATTTACAACATTTAAGCACTTTAATTTACAACA-TTTAAACACTTCAATTTATAGC
1 AACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAACACTTCAATTAACAAC
* * * * *
27411571 ATTTAACACTTCAACTTGCAGCACTTTAACACTTCAATTTATAGCATTTAAACACTTCAATTTGC
66 AATTAACACCTCAACTTACAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTCAATTTGC
27411636 AGCACTTT
131 AGCACTTT
*
27411644 AACACTTCAATTTACAGCATTTAAACACTTCAATTTGCTGCACTTT
1 AACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTT
27411690 CATACCTTCA
Statistics
Matches: 496, Mismatches: 68, Indels: 57
0.80 0.11 0.09
Matches are distributed among these distances:
134 1 0.00
135 110 0.22
136 53 0.11
137 258 0.52
138 69 0.14
139 5 0.01
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (138 bp):
AACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAACACTTCAATTAACAAC
AATTAACACCTCAACTTACAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTCAATTTGC
AGCACTTT
Found at i:27411477 original size:206 final size:204
Alignment explanation
Indices: 27411119--27411632 Score: 782
Period size: 206 Copynumber: 2.5 Consensus size: 204
27411109 TACAGCGATA
* ** * *
27411119 AAACATTTCAATTT-CTAGCAACTAAACACTTCAATTTACAACATTTAAACAC-TCAATTTACAT
1 AAACACTTCAATTTAC-AGCATTTAAACACTTCAATTTACAGCATTT-AACACTTCAATTTACAG
* *
27411182 CATTTAACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTAC
64 CATTTAACACTTCAATTTGCAGCACTTTAACATTTCAATTAACAACAATTATACACCTCAATTAC
*
27411247 AGCGATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAAT
129 AGAGATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAAT
27411312 TTACAACATTT
194 TTACAACATTT
*
27411323 AAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAGC
1 AAACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCA-TTTAACACTTCAATTTACAGC
27411388 ATTTAAACACTTCAATTTGCAGCACTTTAACATTTCAATTAACAACAATTATACACCTCAATTAC
65 ATTT-AACACTTCAATTTGCAGCACTTTAACATTTCAATTAACAACAATTATACACCTCAATTAC
*
27411453 AGATATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAAT
129 AGAGATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAAT
27411518 TTACAACATTT
194 TTACAACATTT
* * * * * *
27411529 AAGCACTTTAATTTACAACATTTAAACACTTCAATTTATAGCATTTAACACTTCAACTTGCAGCA
1 AAACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCATTTAACACTTCAATTTACAGCA
** *
27411594 CTTTAACACTTCAATTTATAGCA-TTTAAACACTTCAATT
66 -TTTAACACTTCAATTTGCAGCACTTT-AACATTTCAATT
27411633 TGCAGCACTT
Statistics
Matches: 284, Mismatches: 20, Indels: 11
0.90 0.06 0.03
Matches are distributed among these distances:
204 44 0.15
205 67 0.24
206 173 0.61
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.33
Consensus pattern (204 bp):
AAACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCATTTAACACTTCAATTTACAGCA
TTTAACACTTCAATTTGCAGCACTTTAACATTTCAATTAACAACAATTATACACCTCAATTACAG
AGATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAATTT
ACAACATTT
Found at i:27411497 original size:91 final size:91
Alignment explanation
Indices: 27410986--27411689 Score: 384
Period size: 91 Copynumber: 7.7 Consensus size: 91
27410976 GTACTTAAAA
* * * * * * *
27410986 ACTTCAATTTACA-ACATTTAAACA-CTTCAATTTGCAGCACTTTAACACTTCAATTTACAACA-
1 ACTTCAATTTACAGATA-TAAAACATC-TCAATTTACAGCAATTAAACACTTCAATTTGCAGCAC
* * *
27411048 TTTAAACACTTTAATTTGCAGCACTTTAAC
64 TTT-AACACTTCAATTTACAACA-TTTAAC
* * * * * * *
27411078 A-TCTCAATTAACA-ACATTTATAC-TCCTCAA-TTACAGCGATAAAACATTTCAATTT-CTAGC
1 ACT-TCAATTTACAGATA-TAAAACAT-CTCAATTTACAGCAATTAAACACTTCAATTTGC-AGC
*
27411138 AAC-TAAACACTTCAATTTACAACATTTAAAC
62 -ACTTTAACACTTCAATTTACAACATTT-AAC
* * * * * * ** *
27411169 AC-TCAATTTACATCATTTAACAC-T-TCAATTTGCAGCACTTTAACA-TCTCAATTAACAACA-
1 ACTTCAATTTACA-GATATAAAACATCTCAATTTACAGCAATTAAACACT-TCAATTTGCAGCAC
* * **
27411229 TTTATACACCTCAA-TTACAGCGATAAAAC
64 TTTA-ACACTTCAATTTACAAC-ATTTAAC
* * * * * *
27411258 A-TCTCAATTTCCAGCA-ACT-AAACA-CTTCAATTTGCAGTACTTAAACACTTCAATTTACAAC
1 ACT-TCAATTTACAG-ATA-TAAAACATC-TCAATTTACAGCAATTAAACACTTCAATTTGCAGC
*
27411319 A-TTTAAACACTTCAATTTACAGCATTTAAAC
62 ACTTT-AACACTTCAATTTACAACATTT-AAC
* * * *
27411350 ACTTCAATTTGCAGCACTTTAACAC-T-TCAATTTACAGCATTTAAACACTTCAATTTGCAGCAC
1 ACTTCAATTTACAG-A-TATAAAACATCTCAATTTACAGCAATTAAACACTTCAATTTGCAGCAC
* * *
27411413 TTTAACATTTCAATTAACAACAATTATAC
64 TTTAACACTTCAATTTACAACATTTA-AC
* * * *
27411442 ACCTCAA-TTACAGATATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTT
1 ACTTCAATTTACAGATATAAAACATCTCAATTTACAGCAATTAAACACTTCAATTTGCAGCACTT
*
27411506 AAACACTTCAATTTACAACATTTAAGC
66 TAACACTTCAATTTACAACATTTAA-C
* * * * * *
27411533 ACTTTAATTTACA-ACATTTAAACA-CTTCAATTTATAGC-ATTTAACACTTCAACTTGCAGCAC
1 ACTTCAATTTACAGATA-TAAAACATC-TCAATTTACAGCAATTAAACACTTCAATTTGCAGCAC
* *
27411595 TTTAACACTTCAATTTATAGCATTTAAAC
64 TTTAACACTTCAATTTACAACATTT-AAC
* * * * *
27411624 ACTTCAATTTGCAGCACTTTAACAC-T-TCAATTTACAGCATTTAAACACTTCAATTTGCTGCAC
1 ACTTCAATTTACAG-A-TATAAAACATCTCAATTTACAGCAATTAAACACTTCAATTTGCAGCAC
27411687 TTT
64 TTT
27411690 CATACCTTCA
Statistics
Matches: 478, Mismatches: 88, Indels: 92
0.73 0.13 0.14
Matches are distributed among these distances:
89 27 0.06
90 56 0.12
91 227 0.47
92 154 0.32
93 11 0.02
94 3 0.01
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (91 bp):
ACTTCAATTTACAGATATAAAACATCTCAATTTACAGCAATTAAACACTTCAATTTGCAGCACTT
TAACACTTCAATTTACAACATTTAAC
Found at i:27411679 original size:114 final size:115
Alignment explanation
Indices: 27410980--27411679 Score: 734
Period size: 114 Copynumber: 6.1 Consensus size: 115
27410970 TTTGCAGTAC
* * *
27410980 TTAAAAACTTCAATTTACAACATTTAAACACTTCAATTTGCAGC-ACTTTAACACTTCAATTTAC
1 TTAAACACTTCAATTTACAGCATTT-AACACTTCAATTTGCAGCAACTTAAACACTTCAATTTAC
* * *
27411044 AACATTTAAACACTTTAATTTGCAGCACTTTAACA-TCTCAATTAACAACAT
65 AGCATTTAAACACTTCAATTTGCAGCACTTTAACACT-TCAATTTACAACAT
* * * ** *
27411095 TTATACTCCTCAA-TTACAGCGATAAAACATTTCAATTT-CTAGCAAC-TAAACACTTCAATTTA
1 TTAAACACTTCAATTTACAGC-ATTTAACACTTCAATTTGC-AGCAACTTAAACACTTCAATTTA
* * * * *
27411157 CAACATTTAAACAC-TCAATTTACATCA-TTTAACACTTCAATTTGCAGCACT
64 CAGCATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAACA-T
* * * * * *
27411208 TT-AACA-TCTCAATTAACAACATTTATACACCTCAA-TTACAGCGA-TAAAACA-TCTCAATTT
1 TTAAACACT-TCAATTTACAGCATTTA-ACACTTCAATTTGCAGCAACTTAAACACT-TCAATTT
* ** * *
27411268 CCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACAT
63 ACAGCATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAACAT
*
27411321 TTAAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGC-ACTTTAACACTTCAATTTAC
1 TTAAACACTTCAATTTACAGCATTT-AACACTTCAATTTGCAGCAACTTAAACACTTCAATTTAC
* * *
27411385 AGCATTTAAACACTTCAATTTGCAGCACTTTAACATTTCAATTAACAACAA
65 AGCATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAACAT
* * * * * *
27411436 TTATACACCTCAA-TTACAG-ATATAAAACATCTCAATTTCCAGCAAC-TAAACACTTCAATTTG
1 TTAAACACTTCAATTTACAGCATTTAACAC-T-TCAATTTGCAGCAACTTAAACACTTCAATTTA
* * * * *
27411498 CAGTACTTAAACACTTCAATTTACAACA-TTTAAGCACTTTAATTTACAACAT
64 CAGCATTTAAACACTTCAATTTGCAGCACTTTAA-CACTTCAATTTACAACAT
* * * *
27411550 TTAAACACTTCAATTTATAGCATTTAACACTTCAACTTGCAGC-ACTTTAACACTTCAATTTATA
1 TTAAACACTTCAATTTACAGCATTTAACACTTCAATTTGCAGCAACTTAAACACTTCAATTTACA
*
27411614 GCATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAGCAT
66 GCATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAACAT
27411664 TTAAACACTTCAATTT
1 TTAAACACTTCAATTT
27411680 GCTGCACTTT
Statistics
Matches: 477, Mismatches: 81, Indels: 55
0.78 0.13 0.09
Matches are distributed among these distances:
111 1 0.00
112 59 0.12
113 52 0.11
114 255 0.53
115 102 0.21
116 8 0.02
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (115 bp):
TTAAACACTTCAATTTACAGCATTTAACACTTCAATTTGCAGCAACTTAAACACTTCAATTTACA
GCATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAACAT
Found at i:27411689 original size:46 final size:45
Alignment explanation
Indices: 27410960--27411679 Score: 606
Period size: 46 Copynumber: 15.8 Consensus size: 45
27410950 TCAGCAACTA
* * * * * *
27410960 AACAATTCAATTTGCAGTACTTAAAAACTTCAATTTACAACATTT
1 AACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCATTT
* *
27411005 AAACACTTCAATTTGCAGCACTTT-AACACTTCAATTTACAACATTT
1 -AACACTTCAATTTACAGCA-TTTAAACACTTCAATTTACAGCATTT
* * * *
27411051 AAACACTTTAATTTGCAGCACTTT-AACA-TCTCAATTAACAACATTT
1 -AACACTTCAATTTACAGCA-TTTAAACACT-TCAATTTACAGCATTT
* * * * * *
27411097 ATACTCCTCAA-TTACAGCGA-TAAAACATTTCAATTT-CTAGCAACTA
1 A-ACACTTCAATTTACAGC-ATTTAAACACTTCAATTTAC-AGC-ATTT
* *
27411143 AACACTTCAATTTACAACATTTAAACAC-TCAATTTACATCATTT
1 AACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCATTT
* * *
27411187 AACACTTCAATTTGCAGCACTTT-AACA-TCTCAATTAACAACATTT
1 AACACTTCAATTTACAGCA-TTTAAACACT-TCAATTTACAGCATTT
* * * * *
27411232 ATACACCTCAA-TTACAGCGA-TAAAACA-TCTCAATTTCCAGCAACTA
1 A-ACACTTCAATTTACAGC-ATTTAAACACT-TCAATTTACAGC-ATTT
* * * *
27411278 AACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTT
1 AACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCATTT
*
27411323 AAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTT
1 -AACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCA-TTT
*
27411370 AACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTT
1 AACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCA-TTT
* * * * * * *
27411416 AACATTTCAATTAACAACAATTATACACCTCAA-TTACAG-ATAT
1 AACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCATTT
* * ** * * *
27411459 AAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTTA
1 AACAC-T-TCAATTTACAGCATTTAAACACTTCAATTTACAGCA-TTT
* * * *
27411507 AACACTTCAATTTACAACATTTAAGCACTTTAATTTACAACATTT
1 AACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCATTT
* * *
27411552 AAACACTTCAATTTATAGCATTT-AACACTTCAACTTGCAGCACTTT
1 -AACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCA-TTT
* *
27411598 AACACTTCAATTTATAGCATTTAAACACTTCAATTTGCAGCACTTT
1 AACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCA-TTT
27411644 AACACTTCAATTTACAGCATTTAAACACTTCAATTT
1 AACACTTCAATTTACAGCATTTAAACACTTCAATTT
27411680 GCTGCACTTT
Statistics
Matches: 556, Mismatches: 87, Indels: 62
0.79 0.12 0.09
Matches are distributed among these distances:
43 5 0.01
44 28 0.05
45 151 0.27
46 359 0.65
47 8 0.01
48 5 0.01
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (45 bp):
AACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCATTT
Found at i:27413367 original size:34 final size:34
Alignment explanation
Indices: 27413322--27413392 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
27413312 GAGCTTGGAG
*
27413322 ACGCTGCTGGAGAGTTTCTTGATTGAAAAGAGCA
1 ACGCTGCTGGAGAATTTCTTGATTGAAAAGAGCA
*
27413356 ACGCTGTTGGAGAATTTCTTGATTGAAAAGAGCA
1 ACGCTGCTGGAGAATTTCTTGATTGAAAAGAGCA
27413390 ACG
1 ACG
27413393 GAGGGGTGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (34 bp):
ACGCTGCTGGAGAATTTCTTGATTGAAAAGAGCA
Found at i:27414080 original size:14 final size:15
Alignment explanation
Indices: 27414061--27414095 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
27414051 TTTAATTTTC
27414061 AAAATTTCAAAAA-A
1 AAAATTTCAAAAATA
*
27414075 AAAATTTTAAAAATA
1 AAAATTTCAAAAATA
27414090 AAAATT
1 AAAATT
27414096 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTTCAAAAATA
Found at i:27414125 original size:30 final size:31
Alignment explanation
Indices: 27414091--27414192 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
27414081 TTAAAAATAA
*
27414091 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
27414121 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
27414151 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
27414181 AAATTTCATTTT
1 AAATTTCATTTT
27414193 AATCCTGAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:27414569 original size:3 final size:3
Alignment explanation
Indices: 27414563--27414620 Score: 50
Period size: 3 Copynumber: 19.0 Consensus size: 3
27414553 GCTAGACTTT
27414563 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAAA GAAA GAA -AA -AA GAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA G-AA G-AA GAA GAA GAA GAA
*
27414610 AAA GAA -AA GAA
1 GAA GAA GAA GAA
27414621 ATAATAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 6 0.12
3 29 0.60
4 13 0.27
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:27414581 original size:10 final size:10
Alignment explanation
Indices: 27414566--27414594 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
27414556 AGACTTTGAA
27414566 GAAGAAGAAG
1 GAAGAAGAAG
27414576 GAAGAAGAAG
1 GAAGAAGAAG
27414586 GAAGAAGAA
1 GAAGAAGAA
27414595 AGAAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:27414597 original size:7 final size:7
Alignment explanation
Indices: 27414563--27414616 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
27414553 GCTAGACTTT
27414563 GAAG-AA
1 GAAGAAA
*
27414569 GAAGAAG
1 GAAGAAA
27414576 GAAG-AA
1 GAAGAAA
*
27414582 GAAGGAA
1 GAAGAAA
27414589 GAAGAAA
1 GAAGAAA
27414596 GAAAGAAA
1 G-AAGAAA
*
27414604 AAAGAAA
1 GAAGAAA
27414611 -AAGAAA
1 GAAGAAA
27414617 AGAAATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 15 0.37
7 20 0.49
8 6 0.15
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (7 bp):
GAAGAAA
Found at i:27414907 original size:11 final size:10
Alignment explanation
Indices: 27414885--27414952 Score: 73
Period size: 11 Copynumber: 6.3 Consensus size: 10
27414875 GGCCCAGCAG
27414885 AGAAAAAAAA
1 AGAAAAAAAA
27414895 AGAAAAGAAAA
1 AGAAAA-AAAA
*
27414906 AGAAGAAAAAG
1 AGAA-AAAAAA
*
27414917 AGAAGGAAAAA
1 AGAA-AAAAAA
27414928 AGAAGGAAAAAA
1 AGAA--AAAAAA
27414940 AGAAAAAAAA
1 AGAAAAAAAA
27414950 AGA
1 AGA
27414953 GGTTCAATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
10 15 0.29
11 24 0.47
12 12 0.24
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:27415114 original size:17 final size:16
Alignment explanation
Indices: 27415085--27415129 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
27415075 TGCATACTTA
27415085 TATTTATATTTTTAATT
1 TATTTA-ATTTTTAATT
27415102 TAATTTAATTTTTAATT
1 T-ATTTAATTTTTAATT
*
27415119 TATTTTATTTT
1 TATTTAATTTT
27415130 AAATAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 9 0.35
17 12 0.46
18 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTAATTTTTAATT
Found at i:27415358 original size:17 final size:17
Alignment explanation
Indices: 27415271--27415790 Score: 136
Period size: 17 Copynumber: 29.5 Consensus size: 17
27415261 AAAATTGTAA
* *
27415271 TTTCAATAATCCTCGTG
1 TTTCAAAAATTCTCGTG
* *
27415288 CTTTTAAAAATTCTCATG
1 -TTTCAAAAATTCTCGTG
27415306 TTTCAAAAA-TCTTCGTG
1 TTTCAAAAATTC-TCGTG
* *
27415323 TTTTAAAAATTCTAGTG
1 TTTCAAAAATTCTCGTG
* *
27415340 TTTCAAAAATTTTCTTG
1 TTTCAAAAATTCTCGTG
*
27415357 TTTTCAGAAAAAATTTTCGTG
1 -TTTC---AAAAATTCTCGTG
* * * *
27415378 TTTTATAAATT-TCCATAT
1 TTTCAAAAATTCT-CGT-G
* *
27415396 TTTCAAAAAAATCAT-GTC
1 TTTC-AAAAATTC-TCGTG
*
27415414 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
*
27415431 TTTTCAAAAAAAAATGAC-CGTG
1 -TTTC----AAAAAT-TCTCGTG
27415453 TTTCAAAAATT-TCCGTG
1 TTTCAAAAATTCT-CGTG
** * *
27415470 TTAAAAAAAAAATCTTCGTAT
1 TT--TCAAAAATTC-TCGT-G
*
27415491 TTTCAAAAAATTTTCGTG
1 TTTC-AAAAATTCTCGTG
27415509 TTTTCAAAAATT-TCGGTG
1 -TTTCAAAAATTCTC-GTG
* *
27415527 TTTCAAAGATTTTCGTG
1 TTTCAAAAATTCTCGTG
*
27415544 TTTTCAAAAACTC-CGGTG
1 -TTTCAAAAATTCTC-GTG
* *** *
27415562 ATTTTTAAAAAAAAATCAT-
1 ---TTTCAAAAATTCTCGTG
27415581 TTTCTAAAAAATT-TCCGTG
1 TTTC--AAAAATTCT-CGTG
*
27415600 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
* *
27415617 TTTTAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
* *
27415634 TTTTAAAAATTCTCGTA
1 TTTCAAAAATTCTCGTG
* *
27415651 TTT--TAAATT-T--TT
1 TTTCAAAAATTCTCGTG
* *** *
27415663 TTTAAGAAAAAAATTGTG
1 TTTCA-AAAATTCTCGTG
* * *
27415681 TTTCAAAAAATGTCTTG
1 TTTCAAAAATTCTCGTG
*
27415698 TTTTAAAAATTCTCGTG
1 TTTCAAAAATTCTCGTG
* *
27415715 TTTCAAAAAATGTCGTG
1 TTTCAAAAATTCTCGTG
* *
27415732 TTTTAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
**
27415749 TTTCTGAAATT-TCCGTG
1 TTTCAAAAATTCT-CGTG
*
27415766 TTT-AAAAATTCTTGTG
1 TTTCAAAAATTCTCGTG
*
27415782 TTTTAAAAA
1 TTTCAAAAA
27415791 AACTTTCATT
Statistics
Matches: 374, Mismatches: 80, Indels: 97
0.68 0.15 0.18
Matches are distributed among these distances:
12 4 0.01
14 1 0.00
15 8 0.02
16 20 0.05
17 197 0.53
18 67 0.18
19 24 0.06
20 22 0.06
21 21 0.06
22 10 0.03
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (17 bp):
TTTCAAAAATTCTCGTG
Found at i:27415499 original size:57 final size:58
Alignment explanation
Indices: 27415418--27415528 Score: 136
Period size: 57 Copynumber: 1.9 Consensus size: 58
27415408 CATGTCTTTC
* *
27415418 AAAAATTTTCGTGTTTTCAAAAAAAAATGACCGTG-TTTCAAAAATTTCCGTGTTAAAAA
1 AAAAATCTTCGTATTTTC--AAAAAAATGACCGTGTTTTCAAAAATTTCCGTGTTAAAAA
*** *
27415477 AAAAATCTTCGTATTTTC-AAAAAATTTTCGTGTTTTCAAAAATTTCGGTGTT
1 AAAAATCTTCGTATTTTCAAAAAAATGACCGTGTTTTCAAAAATTTCCGTGTT
27415529 TCAAAGATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 11 0.24
57 18 0.40
59 16 0.36
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (58 bp):
AAAAATCTTCGTATTTTCAAAAAAATGACCGTGTTTTCAAAAATTTCCGTGTTAAAAA
Found at i:27415625 original size:34 final size:34
Alignment explanation
Indices: 27415283--27415790 Score: 193
Period size: 34 Copynumber: 14.4 Consensus size: 34
27415273 TCAATAATCC
* *
27415283 TCGTGCTTTTAAAAA-TTCTCATGTTTCAAAAATCT
1 TCGTG-TTTTAAAAATTTC-CGTGTTTCAAAAATTT
*
27415318 TCGTGTTTTAAAAA-TTCTAGTGTTTCAAAAATTT
1 TCGTGTTTTAAAAATTTC-CGTGTTTCAAAAATTT
* * * *
27415352 TCTTGTTTTCAGAAAAAATTTTCGTGTTTTATAAATTT
1 TCGTGTTTT----AAAAATTTCCGTGTTTCAAAAATTT
* * * ** * *
27415390 CCATATTTTCAAAAAAATCATGTCTTTCAAAAATTT
1 TCGTGTTTT-AAAAATTTC-CGTGTTTCAAAAATTT
**
27415426 TCGTGTTTTCAAAAAAAAATGACCGTGTTTCAAAAATTT
1 TCGTGTTTT-----AAAAATTTCCGTGTTTCAAAAATTT
* ** *
27415465 CCGTGTTAAAAAAAAAATCTT-CGTATTTTCAAAAAATTT
1 TCGTGTT---TTAAAAAT-TTCCGT-GTTTC-AAAAATTT
* *
27415504 TCGTGTTTTCAAAAATTTCGGTGTTTCAAAGATTT
1 TCGTGTTTT-AAAAATTTCCGTGTTTCAAAAATTT
* * ***
27415539 TCGTGTTTTCAAAAA-CTCCGGTGATTTTTAAAAAAAAA
1 TCGTGTTTT-AAAAATTTCC-GTG---TTTCAAAAATTT
*
27415577 TCAT-TTTCTAAAAAATTTCCGTGTTTCAAAAATTT
1 TCGTGTTT-T-AAAAATTTCCGTGTTTCAAAAATTT
* * *
27415612 TCGTGTTTTAAAAATTTTCGTGTTTTAAAAATTC
1 TCGTGTTTTAAAAATTTCCGTGTTTCAAAAATTT
* * * **
27415646 TCGTATTTT--AAATTT---TTTTTAAGAAAAAAAT
1 TCGTGTTTTAAAAATTTCCGTGTTT--CAAAAATTT
* * * * *
27415677 T-GTGTTTCAAAAAATGT-CTTGTTTTAAAAATTC
1 TCGTGTTT-TAAAAATTTCCGTGTTTCAAAAATTT
* * *
27415710 TCGTGTTTCAAAAAATGT-CGTGTTTTAAAAATTT
1 TCGTGTTT-TAAAAATTTCCGTGTTTCAAAAATTT
*
27415744 TCGTGTTTCT-GAAATTTCCGTGTTT-AAAAATTCT
1 TCGTGTTT-TAAAAATTTCCGTGTTTCAAAAATT-T
27415778 T-GTGTTTTAAAAA
1 TCGTGTTTTAAAAA
27415791 AACTTTCATT
Statistics
Matches: 359, Mismatches: 78, Indels: 74
0.70 0.15 0.14
Matches are distributed among these distances:
29 4 0.01
30 5 0.01
31 6 0.02
32 7 0.02
33 32 0.09
34 114 0.32
35 52 0.14
36 27 0.08
37 20 0.06
38 47 0.13
39 39 0.11
40 6 0.02
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (34 bp):
TCGTGTTTTAAAAATTTCCGTGTTTCAAAAATTT
Found at i:27429499 original size:3 final size:3
Alignment explanation
Indices: 27429493--27429527 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
27429483 TAACCTTTTT
27429493 TTC TTC TTC TTC TTC TTTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC T
27429528 CTTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:27429513 original size:16 final size:16
Alignment explanation
Indices: 27429492--27429530 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
27429482 CTAACCTTTT
27429492 TTTCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTC
27429508 TTTCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTC
27429524 TTCTCTT
1 TT-TCTT
27429531 TTTTTTTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTCTTCTTCTTCTTC
Found at i:27436336 original size:48 final size:48
Alignment explanation
Indices: 27436237--27436336 Score: 119
Period size: 48 Copynumber: 2.1 Consensus size: 48
27436227 CAGTGACCCG
* * * * *
27436237 ACTACAATGGTTTATACCATTCAATATATTACTATCAGGGATGGCCCA
1 ACTACAATGGTTTATACCATTCAATATACTACCATCAGAGATAGCCAA
* * **
27436285 ACTACAATGGTTTATACCCTTTAATATACTACCATCCTAGATAGCCAA
1 ACTACAATGGTTTATACCATTCAATATACTACCATCAGAGATAGCCAA
27436333 ACTA
1 ACTA
27436337 TGATGGCTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (48 bp):
ACTACAATGGTTTATACCATTCAATATACTACCATCAGAGATAGCCAA
Found at i:27437461 original size:21 final size:21
Alignment explanation
Indices: 27437437--27437506 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
27437427 ATCCCTGGTC
27437437 CACACGGGCGTGTGCTCTCTT
1 CACACGGGCGTGTGCTCTCTT
* * *
27437458 CACAAGAGCGTGTGCTCAGC--
1 CACACGGGCGTGTGCTC-TCTT
* *
27437478 CACACGGCCGTGTGCCCCTCTT
1 CACACGGGCGTGTG-CTCTCTT
27437500 CACACGG
1 CACACGG
27437507 ACTTTTGACC
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
20 12 0.32
21 17 0.46
22 8 0.22
ACGTcount: A:0.16, C:0.37, G:0.27, T:0.20
Consensus pattern (21 bp):
CACACGGGCGTGTGCTCTCTT
Found at i:27439801 original size:14 final size:15
Alignment explanation
Indices: 27439782--27439816 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
27439772 GTTAATTTTC
*
27439782 AAAATTTCAAAAA-A
1 AAAATTTAAAAAATA
27439796 AAAATTTAAAAAATA
1 AAAATTTAAAAAATA
27439811 AAAATT
1 AAAATT
27439817 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTAAAAAATA
Found at i:27439873 original size:29 final size:30
Alignment explanation
Indices: 27439812--27439912 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
27439802 TAAAAAATAA
* *
27439812 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-TT
*
27439842 AAATTTCATTTTGA-CCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* * *
27439871 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
27439901 AAATTTCATTTT
1 AAATTTCATTTT
27439913 AATCCTAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
29 23 0.38
30 37 0.62
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.45
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTTT
Found at i:27439934 original size:59 final size:59
Alignment explanation
Indices: 27439809--27439934 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 59
27439799 ATTTAAAAAA
* * *
27439809 TAAAAATTGCATTTTGACCCCTAAACTTTTCCTAAATTTCATTTTGACCTTAAACTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAAATTTCATTTTAACCTTAAACTTTC
** * * *
27439868 TTTAAATTTCACTTAGACCCCTAAAC-TTTCATTAAATTTCATTTTAATCC-TAAATTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTC-CTAAATTTCATTTTAA-CCTTAAACTTTC
27439927 TAAAAATT
1 TAAAAATT
27439935 ACATTTAGCC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 4 0.07
59 49 0.89
60 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.44
Consensus pattern (59 bp):
TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAAATTTCATTTTAACCTTAAACTTTC
Found at i:27440190 original size:20 final size:20
Alignment explanation
Indices: 27440167--27440208 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
27440157 TTTCGAAAAA
27440167 AAAGA-AGAAAAGAAAAAGAG
1 AAAGAGAGAAAA-AAAAAGAG
27440187 AAAGAGGAGAAAAAAAAAGAG
1 AAAGA-GAGAAAAAAAAAGAG
27440208 A
1 A
27440209 CCGGCGTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAGAGAGAAAAAAAAAGAG
Found at i:27440261 original size:3 final size:3
Alignment explanation
Indices: 27440255--27440308 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
27440245 AGGCTAACTT
* * * *
27440255 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA AAA GAA AAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
27440303 AAA GAA
1 GAA GAA
27440309 AAAAATAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:27440323 original size:24 final size:24
Alignment explanation
Indices: 27440256--27440313 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
27440246 GGCTAACTTG
* * * * *
27440256 AAGAAGAAGAAGAAGAAGAAGAAG
1 AAGAAAAAAAAGAAAAAAAAGAAA
27440280 AAGAAAAAAAAGAAAAAAAAGAAA
1 AAGAAAAAAAAGAAAAAAAAGAAA
27440304 AAGAAAAAAA
1 AAGAAAAAAA
27440314 TAATAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (24 bp):
AAGAAAAAAAAGAAAAAAAAGAAA
Found at i:27440578 original size:19 final size:18
Alignment explanation
Indices: 27440554--27440608 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
27440544 CCACAGAGAA
27440554 AAAAAGAAAAGAAAATAAG
1 AAAAAGAAAAGAAAA-AAG
*
27440573 AAAAAGAGAAGGAAAAAAG
1 AAAAAGA-AAAGAAAAAAG
27440592 AAGAAA-AAAAGAAAAAA
1 AA-AAAGAAAAGAAAAAA
27440609 AAGGTCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 9 0.28
19 13 0.41
20 10 0.31
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAAG
Found at i:27440609 original size:11 final size:11
Alignment explanation
Indices: 27440550--27440610 Score: 72
Period size: 11 Copynumber: 5.7 Consensus size: 11
27440540 TTGGCCACAG
27440550 AGAAAAAAAGA
1 AGAAAAAAAGA
* *
27440561 A-AAGAAAATA
1 AGAAAAAAAGA
*
27440571 AGAAAAAGAGA
1 AGAAAAAAAGA
*
27440582 AGGAAAAAAGA
1 AGAAAAAAAGA
27440593 AGAAAAAAAGA
1 AGAAAAAAAGA
27440604 A-AAAAAA
1 AGAAAAAA
27440611 GGTCAATTCG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
10 14 0.34
11 27 0.66
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAGA
Found at i:27440775 original size:16 final size:17
Alignment explanation
Indices: 27440749--27440786 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
27440739 TTATATTTAT
27440749 ATTTTTAATTTAATTTG
1 ATTTTTAATTTAATTTG
* *
27440766 ATTTTT-ATTTTATTTT
1 ATTTTTAATTTAATTTG
27440782 ATTTT
1 ATTTT
27440787 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTAATTTAATTTG
Found at i:27440977 original size:16 final size:16
Alignment explanation
Indices: 27440948--27441000 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
27440938 CGTGCTTTTA
27440948 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
*
27440964 AAAA-TCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
27440981 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
27440997 AAAA
1 AAAA
27441001 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 2 0.06
16 15 0.48
17 12 0.39
18 2 0.06
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:27441002 original size:34 final size:34
Alignment explanation
Indices: 27440925--27441015 Score: 105
Period size: 34 Copynumber: 2.7 Consensus size: 34
27440915 AAAATTGTAA
* * *
27440925 TTTCAATAATCCTCGTGCTTTTAAAAATTCTCATG
1 TTTCAAAAATCTTCGTG-TTTTCAAAATTCTCATG
27440960 TTTC-AAAATCTTCGTGTTTTCAAAATTCT-AGTG
1 TTTCAAAAATCTTCGTGTTTTCAAAATTCTCA-TG
* *
27440993 TTTCAAAAATTTTCTTGTTTTCA
1 TTTCAAAAATCTTCGTGTTTTCA
27441016 GAAAAATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
32 1 0.02
33 18 0.37
34 26 0.53
35 4 0.08
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.47
Consensus pattern (34 bp):
TTTCAAAAATCTTCGTGTTTTCAAAATTCTCATG
Found at i:27441266 original size:17 final size:16
Alignment explanation
Indices: 27440937--27441447 Score: 200
Period size: 17 Copynumber: 29.9 Consensus size: 16
27440927 TCAATAATCC
*
27440937 TCGTGCTTTTAAAAATT
1 TCGTG-TTTCAAAAATT
*
27440954 CTCATGTTTC-AAAATCT
1 -TCGTGTTTCAAAAAT-T
27440971 TCGTGTTTTC-AAAATT
1 TCGTG-TTTCAAAAATT
*
27440987 CTAGTGTTTCAAAAATTT
1 -TCGTGTTTCAAAAA-TT
*
27441005 TCTTGTTTTCAGAAAAATTT
1 TCGTG-TTTC--AAAAA-TT
* *
27441025 TCGTGTTT-TATAATT
1 TCGTGTTTCAAAAATT
* *
27441040 TCCGTATTTTCAAAAAAATC
1 T-CGT-GTTTC--AAAAATT
* *
27441060 ACGTCTTTCAAAAATTT
1 TCGTGTTTCAAAAA-TT
*
27441077 TCGTGTTTTCAAAAAAAATGA
1 TCGTG-TTTC---AAAAAT-T
*
27441098 CCGTGTTTCAAAAATT
1 TCGTGTTTCAAAAATT
**
27441114 TCGTGTTAAAAAAAATCT
1 TCGTGTT-TCAAAAAT-T
*
27441132 TCGTATTTTCAAAAAATTT
1 TCGT-GTTTC-AAAAA-TT
27441151 TCGTGTTTC-AAAATT
1 TCGTGTTTCAAAAATT
27441166 TCGTGTTTTCAAAAATT
1 TCGTG-TTTCAAAAATT
*
27441183 TCGGTGTTTCAAAGATTT
1 TC-GTGTTTCAAA-AATT
*
27441201 TCGTGTTTTCAAAAACT
1 TCGTG-TTTCAAAAATT
* * **
27441218 CCGGTGATTTAAAAAAAAA
1 TC-GTG-TTT-CAAAAATT
27441237 TCGT-TTTCTAAAAATT
1 TCGTGTTTC-AAAAATT
27441253 TCCGTGTTTCAAAAATTT
1 T-CGTGTTTCAAAAA-TT
*
27441271 TC-TGTTTTAAAAATTT
1 TCGTGTTTCAAAAA-TT
*
27441287 TCGTGTTTTAAAAA-T
1 TCGTGTTTCAAAAATT
* **
27441302 TCTTGTATT-TTAAATT
1 TCGTGT-TTCAAAAATT
* * *
27441318 T--TTTTTAAGAAAAAAAT
1 TCGTGTTT---CAAAAATT
*
27441335 T-GTGTTTCAAAAATG
1 TCGTGTTTCAAAAATT
* *
27441350 TCTTGTTTTAAAAATT
1 TCGTGTTTCAAAAATT
*
27441366 CTCGTGTTTCAAAAAATG
1 -TCGTGTTTC-AAAAATT
*
27441384 TCGTGTTTTAAAAATTT
1 TCGTGTTTCAAAAA-TT
**
27441401 TCGTGTTTCTGAAATT
1 TCGTGTTTCAAAAATT
27441417 TCCGTGTTT-AAAAATT
1 T-CGTGTTTCAAAAATT
*
27441433 CTCGTGTTTTAAAAA
1 -TCGTGTTTCAAAAA
27441448 AAAACTTTCA
Statistics
Matches: 378, Mismatches: 65, Indels: 101
0.69 0.12 0.19
Matches are distributed among these distances:
13 2 0.01
14 2 0.01
15 25 0.07
16 98 0.26
17 129 0.34
18 67 0.18
19 24 0.06
20 22 0.06
21 9 0.02
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (16 bp):
TCGTGTTTCAAAAATT
Found at i:27441391 original size:34 final size:34
Alignment explanation
Indices: 27440937--27441448 Score: 229
Period size: 34 Copynumber: 14.9 Consensus size: 34
27440927 TCAATAATCC
*
27440937 TCGTGCTTTTAAAAATTCTCATGTTTC--AAAATCT
1 TCGTG-TTTTAAAAATTCTCGTGTTTCAAAAAAT-T
* * *
27440971 TCGTGTTTTCAAAATTCTAGTGTTTCAAAAATTT
1 TCGTGTTTTAAAAATTCTCGTGTTTCAAAAAATT
* * * *
27441005 TCTTGTTTTCAGAAAAATTTTCGTGTTT--TATAATT
1 TCGTGTTTT---AAAAATTCTCGTGTTTCAAAAAATT
* * * * *
27441040 TCCGTATTTTCAAAAAAATCACGTCTTTCAAAAATTT
1 T-CGTGTTTT--AAAAATTCTCGTGTTTCAAAAAATT
*
27441077 TCGTGTTTTCAAAAAAAATGAC-CGTGTTTC-AAAAATT
1 TCGTGTTTT----AAAAAT-TCTCGTGTTTCAAAAAATT
** * *
27441114 TCGTGTTAAAAAAAATCTTCGTATTTTCAAAAAATTT
1 TCGTGTTTTAAAAATTC-TCGT-GTTTCAAAAAA-TT
*
27441151 TCGTG-TTTCAAAATT-TCGTGTTTTC-AAAAATT
1 TCGTGTTTTAAAAATTCTCGTG-TTTCAAAAAATT
* * * *
27441183 TCGGTGTTTCAAAGATTTTCGTGTTTTC-AAAAACT
1 TC-GTGTTTTAAAAATTCTCGTG-TTTCAAAAAATT
* * *** *
27441218 CCGGTGATTTAAAAAAAAATCGT-TTTCTAAAAATT
1 TC-GTG-TTTTAAAAATTCTCGTGTTTCAAAAAATT
* * * *
27441253 TCCGTGTTTCAAAAATTTTC-TGTTTTAAAAATTT
1 T-CGTGTTTTAAAAATTCTCGTGTTTCAAAAAATT
* * *
27441287 TCGTGTTTTAAAAATTCTTGTATTT---TAAATT
1 TCGTGTTTTAAAAATTCTCGTGTTTCAAAAAATT
*** * *
27441318 T--T-TTTTAAGAAAAAAATTGTGTTTC-AAAAATG
1 TCGTGTTTT-A-AAAATTCTCGTGTTTCAAAAAATT
* *
27441350 TCTTGTTTTAAAAATTCTCGTGTTTCAAAAAATG
1 TCGTGTTTTAAAAATTCTCGTGTTTCAAAAAATT
* **
27441384 TCGTGTTTTAAAAATTTTCGTGTTTC-TGAAATT
1 TCGTGTTTTAAAAATTCTCGTGTTTCAAAAAATT
*
27441417 TCCGTG-TTTAAAAATTCTCGTGTTTTAAAAAA
1 T-CGTGTTTTAAAAATTCTCGTGTTTCAAAAAA
27441449 AAACTTTCAT
Statistics
Matches: 361, Mismatches: 82, Indels: 70
0.70 0.16 0.14
Matches are distributed among these distances:
28 4 0.01
29 2 0.01
30 11 0.03
31 5 0.01
32 10 0.03
33 82 0.23
34 100 0.28
35 59 0.16
36 36 0.10
37 38 0.11
38 13 0.04
39 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (34 bp):
TCGTGTTTTAAAAATTCTCGTGTTTCAAAAAATT
Found at i:27441486 original size:16 final size:17
Alignment explanation
Indices: 27441467--27441503 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
27441457 ATTTTTAAAA
27441467 AAAAATT-TCGTG-CTT
1 AAAAATTCTCGTGTCTT
*
27441482 CAAAATTCTCGTGTCTT
1 AAAAATTCTCGTGTCTT
27441499 AAAAA
1 AAAAA
27441504 AAGTTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.33
16 5 0.28
17 7 0.39
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (17 bp):
AAAAATTCTCGTGTCTT
Found at i:27441486 original size:20 final size:20
Alignment explanation
Indices: 27441426--27441478 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
27441416 TTCCGTGTTT
27441426 AAAAATTCTCGTGTTTTAAAA
1 AAAAATT-TCGTGTTTTAAAA
*
27441447 AAAAACTTTCAT-TTTTAAAA
1 AAAAA-TTTCGTGTTTTAAAA
27441467 AAAAATTTCGTG
1 AAAAATTTCGTG
27441479 CTTCAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 5 0.18
20 13 0.46
21 8 0.29
22 2 0.07
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (20 bp):
AAAAATTTCGTGTTTTAAAA
Found at i:27449921 original size:122 final size:122
Alignment explanation
Indices: 27449795--27450495 Score: 538
Period size: 122 Copynumber: 5.6 Consensus size: 122
27449785 ATTTTTTAAA
27449795 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
27449860 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* ** * ** *
27449917 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTT-
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT-AGTTTA
** ** ** * ***
27449981 T-TTAAAAAAATCAACTCATATTGCGAGAATTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
65 TGTT--TTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT---------TTTA---ATTTTT
*
27450045 AGTTTATGTTT
116 -G-TT-T-TTC
* ** * * ***
27450056 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT---------TTTA---ATTTTT-G-TT-T
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
** ** * * *
27450106 -TTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA
66 GTTTTAAATTGACTCATATTGCGAG--A-G-G-TGAG--TTAAG-C-CTTTTA---ATTTTT---
* *
27450170 TTTTTTAAA
116 GTTTTT--C
27450179 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
27450244 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
27450301 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
27450366 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* * ** * * *
27450423 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATT
1 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCAC--GCCGAGGTATTTTTAGTT
27450488 TATGTTTT
63 TATGTTTT
27450496 TTTCAATCTA
Statistics
Matches: 466, Mismatches: 62, Indels: 99
0.74 0.10 0.16
Matches are distributed among these distances:
121 4 0.01
122 207 0.44
123 106 0.23
124 12 0.03
125 23 0.05
127 16 0.03
129 3 0.01
130 8 0.02
131 2 0.00
132 6 0.01
134 4 0.01
135 13 0.03
136 3 0.01
137 5 0.01
138 2 0.00
139 52 0.11
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (122 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:27450359 original size:192 final size:192
Alignment explanation
Indices: 27449533--27450337 Score: 1576
Period size: 192 Copynumber: 4.2 Consensus size: 192
27449523 CTTTCCAAGG
*
27449533 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGATACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA-TTT
27449598 TTTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
65 TTTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
27449663 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC-TTTAATTTTTGTTTTTC
130 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
27449725 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
27449790 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
27449855 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
27449917 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*
27449982 TTAAAAAAATCAACTCATATTGCGAGAATTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
27450047 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
27450109 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
27450174 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
27450239 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
27450301 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
27450338 GGGGCACGCC
Statistics
Matches: 609, Mismatches: 3, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
191 113 0.19
192 496 0.81
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (192 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:27450500 original size:16 final size:17
Alignment explanation
Indices: 27450479--27450512 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
27450469 TGCTGAGGTA
*
27450479 TTTTCAATTTATG-TTT
1 TTTTCAATCTATGCTTT
27450495 TTTTCAATCTATGCTTT
1 TTTTCAATCTATGCTTT
27450512 T
1 T
27450513 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTCAATCTATGCTTT
Found at i:27450612 original size:176 final size:182
Alignment explanation
Indices: 27450418--27450830 Score: 484
Period size: 193 Copynumber: 2.2 Consensus size: 182
27450408 TAATTTTTGT
**
27450418 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CACACACTGAGGTATTT
* *
27450482 TC-AA-TTT-A-TGTTTTTTTCAATCTATGCT-TTTC-AAAAATCAACTTATATTGCGAGAGGTG
64 TCAAATTTTAATTGTTTTTTTCAATCTATG-TGTTTCAAAAAATCAACTCATATTGCAAGAGGTG
*
27450541 AGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTGCTTTACTAA-TTCTAC
128 AGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTACTTTAC-AATTTCTAC
* *
27450596 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACACTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACACTGAGGTATTTTC
* * *
27450660 AAATTCTGTTTTTAATTTCTGTTTTTTTTAATTTCTGTGTTTCAAAAAAAAATCAACTCATATTG
66 AAA------TTTTAA--T-TGTTTTTTTCAATCTATGTGTTTC---AAAAAATCAACTCATATTG
* * *
27450725 CAAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTAT
119 CAAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTACTTTACAATTTCTAC
*
27450789 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
27450831 TTTAATTTCT
Statistics
Matches: 198, Mismatches: 15, Indels: 27
0.82 0.06 0.11
Matches are distributed among these distances:
176 51 0.26
177 5 0.03
178 5 0.03
184 3 0.02
185 1 0.01
188 1 0.01
189 19 0.10
192 2 0.01
193 78 0.39
195 33 0.17
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (182 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACACTGAGGTATTTTC
AAATTTTAATTGTTTTTTTCAATCTATGTGTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGT
TGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTACTTTACAATTTCTAC
Found at i:27450676 original size:85 final size:88
Alignment explanation
Indices: 27450418--27450676 Score: 300
Period size: 91 Copynumber: 2.9 Consensus size: 88
27450408 TAATTTTTGT
*
27450418 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CACACGCTGAGGTATTT
*
27450482 TCAATTTATGTTTTTTTCAA-TCTATGC
64 TCAATTTCTG-TTTTTT-AATTCTA-GC
* *
27450509 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG---CACGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCACACGCTGAGGTATTT
**
27450571 TCAATTTCTGCTTTACTAATTCTA-C
64 TCAATTTCTG-TTTTTTAATTCTAGC
* * *
27450596 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACACTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
*
27450660 AAATTCTG-TTTTTAATT
66 AATTTCTGTTTTTTAATT
27450677 TCTGTTTTTT
Statistics
Matches: 147, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
84 3 0.02
85 40 0.27
87 28 0.19
88 2 0.01
89 31 0.21
91 41 0.28
93 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (88 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
AATTTCTGTTTTTTAATTCTAGC
Found at i:27450780 original size:14 final size:14
Alignment explanation
Indices: 27450761--27450795 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
27450751 CGCTGAGGTA
27450761 TTTTCAATTTCTAC
1 TTTTCAATTTCTAC
*
27450775 TTTTCAATTTCTAT
1 TTTTCAATTTCTAC
27450789 TTTTCAA
1 TTTTCAA
27450796 AAATCAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:27450858 original size:54 final size:55
Alignment explanation
Indices: 27450774--27450991 Score: 315
Period size: 54 Copynumber: 4.1 Consensus size: 55
27450764 TCAATTTCTA
27450774 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
27450829 CTTTT-AATTTCTATTTTTCAAAAACCAACTCATATTGCGATAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
27450883 C--TT---TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGC
1 CTTTTCAATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
27450934 CTTTTGCAAATTCT-GTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
27450989 CTT
1 CTT
27450992 GGCTCACGTG
Statistics
Matches: 147, Mismatches: 9, Indels: 14
0.86 0.05 0.08
Matches are distributed among these distances:
50 12 0.08
51 33 0.22
52 2 0.01
53 2 0.01
54 48 0.33
55 41 0.28
56 5 0.03
57 4 0.03
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.38
Consensus pattern (55 bp):
CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:27451304 original size:30 final size:30
Alignment explanation
Indices: 27451264--27451365 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
27451254 TTTAAAATAA
* *
27451264 AAATTACATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
27451294 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
27451324 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
27451354 AAATTTCATTTT
1 AAATTTCATTTT
27451366 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 4 0.06
30 58 0.94
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:27451328 original size:60 final size:59
Alignment explanation
Indices: 27451261--27451399 Score: 165
Period size: 60 Copynumber: 2.4 Consensus size: 59
27451251 TTTTTTAAAA
* *
27451261 TAAAAATTACATTTTGACCCCTAAACTTTTC-CTAAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTACATTTAGACCCCTAAAC-TTTCACTAAATTTCATTTTAACCC-TAAACTTTC
** * * * * *
27451321 TTTAAATTTCACTTAGACCCCTAAACTTTCATTAAATTTCATTTTAATCCTAAATTTTC
1 TAAAAATTACATTTAGACCCCTAAACTTTCACTAAATTTCATTTTAACCCTAAACTTTC
27451380 TAAAAATTACATTTAG-CCCC
1 TAAAAATTACATTTAGACCCC
27451400 AGAAGTTTTG
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
58 4 0.06
59 24 0.37
60 37 0.57
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (59 bp):
TAAAAATTACATTTAGACCCCTAAACTTTCACTAAATTTCATTTTAACCCTAAACTTTC
Found at i:27451739 original size:3 final size:3
Alignment explanation
Indices: 27451733--27451803 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
27451723 GCTAGACTTT
*
27451733 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA G-AA
27451780 GAAA GAA -AA -AA GAA -AA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA
27451804 ATAATAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
2 10 0.17
3 36 0.61
4 13 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:27451751 original size:7 final size:6
Alignment explanation
Indices: 27451733--27451803 Score: 62
Period size: 5 Copynumber: 12.0 Consensus size: 6
27451723 GCTAGACTTT
*
27451733 GAAGAA GAAGAA GGAAGAA GAAGGAA GAAGAA -AAGAG GAAGAA GAAAGAAA
1 GAAGAA GAAGAA -GAAGAA GAA-GAA GAAGAA GAAGAA GAAGAA G-AAG-AA
27451784 GAA-AA -AAGAA -AAGAA -AAGAA
1 GAAGAA GAAGAA GAAGAA GAAGAA
27451804 ATAATAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
4 2 0.04
5 18 0.32
6 17 0.30
7 17 0.30
8 3 0.05
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
GAAGAA
Found at i:27451751 original size:13 final size:13
Alignment explanation
Indices: 27451733--27451778 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
27451723 GCTAGACTTT
27451733 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
27451746 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
27451759 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
27451770 GAAGAAGAA
1 GAAGAAGAA
27451779 AGAAAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:27451916 original size:16 final size:17
Alignment explanation
Indices: 27451877--27451918 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
27451867 CCAGCAGCCC
27451877 AAGAAA-AAACAACAAA
1 AAGAAACAAACAACAAA
*
27451893 AACAAAACAAACAA-AAA
1 AA-GAAACAAACAACAAA
27451910 AAGAAACAA
1 AAGAAACAA
27451919 GCCCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 8 0.36
17 8 0.36
18 6 0.27
ACGTcount: A:0.81, C:0.14, G:0.05, T:0.00
Consensus pattern (17 bp):
AAGAAACAAACAACAAA
Found at i:27452084 original size:14 final size:14
Alignment explanation
Indices: 27452065--27452095 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27452055 GGCCCAGCAG
27452065 AGAAAAAAAAGAAA
1 AGAAAAAAAAGAAA
*
27452079 AGAAAAAGAAGAAA
1 AGAAAAAAAAGAAA
27452093 AGA
1 AGA
27452096 GAAGGAAAAA
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAGAAA
Found at i:27452098 original size:10 final size:9
Alignment explanation
Indices: 27452078--27452127 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
27452068 AAAAAAAGAA
27452078 AAGAAAAAG
1 AAGAAAAAG
27452087 AAGAAAAGAG
1 AAGAAAA-AG
27452097 AAGGAAAAAG
1 AA-GAAAAAG
*
27452107 AAGGAAAA-
1 AAGAAAAAG
*
27452115 AAGAAAAAA
1 AAGAAAAAG
27452124 AAGA
1 AAGA
27452128 GGTTCAATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 7 0.19
9 16 0.44
10 8 0.22
11 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:27452126 original size:20 final size:19
Alignment explanation
Indices: 27452065--27452127 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
27452055 GGCCCAGCAG
27452065 AGAA-AAAAAAGAAAAGAAAA
1 AGAAGAAAAAAG-AAA-AAAA
* *
27452085 AGAAGAAAAGAGAAGGAAAA
1 AGAAGAAAAAAGAA-AAAAA
27452105 AGAAGGAAAAAAGAAAAAAA
1 AGAA-GAAAAAAGAAAAAAA
27452125 AGA
1 AGA
27452128 GGTTCAATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (19 bp):
AGAAGAAAAAAGAAAAAAA
Found at i:27452288 original size:17 final size:17
Alignment explanation
Indices: 27452254--27452303 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
27452244 TTTTATGCAT
27452254 ATTTATATTTATATTTTTA
1 ATTTA-ATTTA-ATTTTTA
27452273 ATTTAATTTAATTTTTA
1 ATTTAATTTAATTTTTA
*
27452290 ATTT-ATTTTATTTT
1 ATTTAATTTAATTTT
27452304 AAATAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 9 0.30
17 11 0.37
18 5 0.17
19 5 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTAATTTAATTTTTA
Found at i:27452504 original size:33 final size:34
Alignment explanation
Indices: 27452444--27452611 Score: 110
Period size: 35 Copynumber: 4.8 Consensus size: 34
27452434 AAAATTGTAA
* *
27452444 TTTCAATAATCCTCGTGCTTTTAAAAATTCTCA-TG
1 TTTCAAAAATCTTCGTG-TTTTAAAAATTCT-AGTG
27452479 TTTCAAAAATCTTCGTGTTTT-AAAATTCTAGTG
1 TTTCAAAAATCTTCGTGTTTTAAAAATTCTAGTG
* * * *
27452512 TTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCGTG
1 TTTCAAAAATCTTCGTGTTTT----AAAAATTCTAGTG
* * * * *
27452550 TTTTATAAAT-TTCCGTATTTTCAAAAAATC-ATGTC
1 TTTCAAAAATCTT-CGTGTTTT-AAAAATTCTA-GTG
*
27452585 TTTCAAAAATTTTCGTGTTTTCAAAAA
1 TTTCAAAAATCTTCGTGTTTT-AAAAA
27452612 AAATGACCTT
Statistics
Matches: 106, Mismatches: 18, Indels: 18
0.75 0.13 0.13
Matches are distributed among these distances:
32 1 0.01
33 29 0.27
34 4 0.04
35 44 0.42
36 2 0.02
37 2 0.02
38 24 0.23
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (34 bp):
TTTCAAAAATCTTCGTGTTTTAAAAATTCTAGTG
Found at i:27452512 original size:16 final size:16
Alignment explanation
Indices: 27452467--27452519 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
27452457 CGTGCTTTTA
27452467 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* * *
27452483 AAAAATCTTCGTGTTTT
1 AAAATTC-TAGTGTTTC
27452500 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
27452516 AAAA
1 AAAA
27452520 ATTTTCTTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:27452530 original size:17 final size:17
Alignment explanation
Indices: 27452456--27452950 Score: 205
Period size: 17 Copynumber: 28.8 Consensus size: 17
27452446 TCAATAATCC
* *
27452456 TCGTGCTTTTAAAAATTC
1 TCGTG-TTTCAAAAATTT
* *
27452474 TCATGTTTCAAAAATCT
1 TCGTGTTTCAAAAATTT
* *
27452491 TCGTGTTT-TAAAATTC
1 TCGTGTTTCAAAAATTT
*
27452507 TAGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
*
27452524 TCTTGTTTTCAGAAAAAATTT
1 TCGTG-TTTC---AAAAATTT
* *
27452545 TCGTGTTTTATAAATTT
1 TCGTGTTTCAAAAATTT
* * **
27452562 CCGTATTTTCAAAAAATCA
1 TCGT-GTTTC-AAAAATTT
*
27452581 T-GTCTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
**
27452597 TCGTGTTTTCAAAAAAAATGA
1 TCGTG-TTTC---AAAAATTT
* *
27452618 CCTTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
* ** **
27452635 CCGTGTTAAAAAAAACT
1 TCGTGTTTCAAAAATTT
*
27452652 TCGTATTTTCAAAAAATTT
1 TCGT-GTTTC-AAAAATTT
*
27452671 TCGTGTTTC-AAAATCT
1 TCGTGTTTCAAAAATTT
27452687 TCGTGTTTTCAAAAA-TT
1 TCGTG-TTTCAAAAATTT
* *
27452704 TGGTGTTTCAAAGATTT
1 TCGTGTTTCAAAAATTT
*
27452721 TCGTGTTTTCAAAAA-CT
1 TCGTG-TTTCAAAAATTT
* * ***
27452738 CCGCTGATTTTAAAAAAAAA
1 TCG-TG--TTTCAAAAATTT
27452758 TCGT-TTTCTAAAAAATTT
1 TCGTGTTTC--AAAAATTT
*
27452776 CCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
* *
27452793 TCGTGTTTTAAAAATTC
1 TCGTGTTTCAAAAATTT
* *
27452810 TCGTATTT--TAAA-TT
1 TCGTGTTTCAAAAATTT
* **
27452824 T--T-TTTAAGAAAAAAT
1 TCGTGTTTCA-AAAATTT
*
27452839 T-GTGTTTCAAAAA-TG
1 TCGTGTTTCAAAAATTT
* * *
27452854 TCTTGTTTTAAAAATTC
1 TCGTGTTTCAAAAATTT
*
27452871 TCGTGTTTCAAAAAATGT
1 TCGTGTTTC-AAAAATTT
*
27452889 T-GTGTTTTAAAAATTT
1 TCGTGTTTCAAAAATTT
*
27452905 TCGTGTTTC-TAAATTT
1 TCGTGTTTCAAAAATTT
* *
27452921 CCGTGTTT-AAAAATTC
1 TCGTGTTTCAAAAATTT
*
27452937 TCGTGTTTTAAAAA
1 TCGTGTTTCAAAAA
27452951 AAACTTTCAT
Statistics
Matches: 353, Mismatches: 88, Indels: 73
0.69 0.17 0.14
Matches are distributed among these distances:
11 3 0.01
12 1 0.00
14 5 0.01
15 6 0.02
16 89 0.25
17 138 0.39
18 52 0.15
19 29 0.08
20 9 0.03
21 21 0.06
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:27452640 original size:38 final size:35
Alignment explanation
Indices: 27452510--27452641 Score: 104
Period size: 38 Copynumber: 3.6 Consensus size: 35
27452500 AAAATTCTAG
* * * *
27452510 TGTTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCG
1 TGTTTCAAAAATTTCCGTGTTTTCA-AAAAAA--TCCT
* * * *
27452548 TGTTTTATAAATTTCCGTATTTTC-AAAAAATCAT
1 TGTTTCAAAAATTTCCGTGTTTTCAAAAAAATCCT
* *
27452582 GTCTTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCT
1 -TGTTTCAAAAATTTCCGTGTTTTC-AAAAAAAT--CCT
27452621 TGTTTCAAAAATTTCCGTGTT
1 TGTTTCAAAAATTTCCGTGTT
27452642 AAAAAAAACT
Statistics
Matches: 73, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
34 1 0.01
35 19 0.26
36 6 0.08
37 7 0.10
38 38 0.52
39 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.45
Consensus pattern (35 bp):
TGTTTCAAAAATTTCCGTGTTTTCAAAAAAATCCT
Found at i:27452649 original size:73 final size:73
Alignment explanation
Indices: 27452512--27452683 Score: 177
Period size: 73 Copynumber: 2.4 Consensus size: 73
27452502 AATTCTAGTG
* * *** * * ***
27452512 TTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCGTGTTTTATAAATTTCCGTATTTTCAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTATTAAAAAAAA
*
27452577 -ATCATGT
66 CATCATAT
* *
27452584 CTTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCTTGTTTCAAAAATTTCCGTGTTAAAAAAA
1 -TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTATTAAAAAAA
* *
27452649 ACTTCGTAT
65 ACATCATAT
27452658 TTTCAAAAAATTTTCGTG-TTTCAAAA
1 TTTC-AAAAATTTTCGTGTTTTCAAAA
27452684 TCTTCGTGTT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
73 65 0.79
74 17 0.21
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (73 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTATTAAAAAAAA
CATCATAT
Found at i:27452662 original size:35 final size:34
Alignment explanation
Indices: 27452623--27452704 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 34
27452613 AATGACCTTG
27452623 TTTCAAAAATTTCCGTGTTAAAAAAAACTTCGTAT
1 TTTCAAAAATTTCCGTGTT-AAAAAAACTTCGTAT
* ** * *
27452658 TTTCAAAAAATTTTCGTGTTTCAAAATCTTCGTGT
1 TTTC-AAAAATTTCCGTGTTAAAAAAACTTCGTAT
27452693 TTTCAAAAATTT
1 TTTCAAAAATTT
27452705 GGTGTTTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 8 0.20
35 19 0.46
36 14 0.34
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (34 bp):
TTTCAAAAATTTCCGTGTTAAAAAAACTTCGTAT
Found at i:27452683 original size:16 final size:16
Alignment explanation
Indices: 27452664--27452949 Score: 91
Period size: 16 Copynumber: 17.2 Consensus size: 16
27452654 GTATTTTCAA
27452664 AAAATTTTCGTGTTTC
1 AAAATTTTCGTGTTTC
*
27452680 AAAATCTTCGTGTTTTC
1 AAAATTTTCGTG-TTTC
* *
27452697 AAAAATTTGGTGTTTC
1 AAAATTTTCGTGTTTC
27452713 AAAGATTTTCGTGTTTTC
1 AAA-ATTTTCGTG-TTTC
** * *
27452731 AAAAACTCCGCTGATTTTAA
1 AAAATTTTCG-TG--TTT-C
***
27452751 AAAAAAATCGT-TTTC
1 AAAATTTTCGTGTTTC
*
27452766 TAAAAAATTTCCGTGTTTC
1 ---AAAATTTTCGTGTTTC
*
27452785 AAAAATTTTCGTGTTTTA
1 -AAAATTTTCGTG-TTTC
* *
27452803 AAAATTCTCGTATTT-
1 AAAATTTTCGTGTTTC
* **
27452818 TAAATTTT--T-TTAAG
1 AAAATTTTCGTGTT-TC
**
27452832 AAAAAATT-GTGTTTC
1 AAAATTTTCGTGTTTC
* * * *
27452847 AAAAATGTCTTGTTTTA
1 AAAATTTTCGTG-TTTC
*
27452864 AAAATTCTCGTGTTTC
1 AAAATTTTCGTGTTTC
* *
27452880 AAAAAATGTT-GTGTTTTA
1 --AAAATTTTCGTG-TTTC
27452898 AAAATTTTCGTGTTTC
1 AAAATTTTCGTGTTTC
* * *
27452914 TAAATTTCCGTGTTTA
1 AAAATTTTCGTGTTTC
* *
27452930 AAAATTCTCGTGTTTT
1 AAAATTTTCGTGTTTC
27452946 AAAA
1 AAAA
27452950 AAAACTTTCA
Statistics
Matches: 199, Mismatches: 50, Indels: 42
0.68 0.17 0.14
Matches are distributed among these distances:
12 2 0.01
13 1 0.01
14 5 0.03
15 13 0.07
16 70 0.35
17 64 0.32
18 28 0.14
19 9 0.05
20 7 0.04
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.45
Consensus pattern (16 bp):
AAAATTTTCGTGTTTC
Found at i:27453727 original size:7 final size:7
Alignment explanation
Indices: 27453715--27453892 Score: 67
Period size: 7 Copynumber: 24.9 Consensus size: 7
27453705 ACTAATTAAT
27453715 CTAAACC
1 CTAAACC
27453722 CTAAACCC
1 CTAAA-CC
*
27453730 CTTAACC
1 CTAAACC
** *
27453737 CATATTCT
1 C-TAAACC
*
27453745 CTAAATC
1 CTAAACC
* *
27453752 ATAAAAC
1 CTAAACC
27453759 CTAAACC
1 CTAAACC
27453766 CTAAACC
1 CTAAACC
27453773 CTAAACC
1 CTAAACC
*
27453780 CATAACCC
1 C-TAAACC
27453788 CT-AACC
1 CTAAACC
*
27453794 CTTAACTC
1 CTAAAC-C
* *
27453802 ATAAACA
1 CTAAACC
*
27453809 TTAAACC
1 CTAAACC
*
27453816 C-CAACC
1 CTAAACC
27453822 CTTAAACC
1 C-TAAACC
* *
27453830 ATAATCC
1 CTAAACC
*
27453837 ATAAACC
1 CTAAACC
*
27453844 TTAAA--
1 CTAAACC
* *
27453849 ATAGTATCTC
1 CTA--AAC-C
*
27453859 ATAAACC
1 CTAAACC
*
27453866 TTAAACC
1 CTAAACC
27453873 CTAAACC
1 CTAAACC
27453880 CTAAACC
1 CTAAACC
27453887 CTAAAC
1 CTAAAC
27453893 TATAATAGTA
Statistics
Matches: 127, Mismatches: 32, Indels: 24
0.69 0.17 0.13
Matches are distributed among these distances:
5 2 0.02
6 10 0.08
7 86 0.68
8 26 0.20
10 3 0.02
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:27455776 original size:8 final size:8
Alignment explanation
Indices: 27455763--27455790 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
27455753 TGGATTTTGA
27455763 GTATAAAT
1 GTATAAAT
27455771 GTATAAAT
1 GTATAAAT
27455779 GTATAAAT
1 GTATAAAT
27455787 GTAT
1 GTAT
27455791 GTGAATGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (8 bp):
GTATAAAT
Found at i:27469459 original size:35 final size:35
Alignment explanation
Indices: 27469317--27469447 Score: 138
Period size: 35 Copynumber: 3.6 Consensus size: 35
27469307 CTTCATTGAA
* * * *
27469317 ATACCATACCTAGATTTTACAACTCGGTATGGGA-A
1 ATACCATACCTACATTTCACAACTCAGTAT-GGATG
* **
27469352 ATGCCATACCTACATTTCTTAACTCAGTATGGATTTG
1 ATACCATACCTACATTTCACAACTCAGTATGGA--TG
27469389 ATAATACCATACCTACATTTCACAACTCAGTATGGATG
1 ---ATACCATACCTACATTTCACAACTCAGTATGGATG
27469427 ATACCATACCTACATTTCACA
1 ATACCATACCTACATTTCACA
27469448 CTTTTCCATG
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
34 3 0.04
35 45 0.56
38 2 0.03
40 30 0.38
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (35 bp):
ATACCATACCTACATTTCACAACTCAGTATGGATG
Found at i:27472369 original size:7 final size:6
Alignment explanation
Indices: 27472328--27472368 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
27472318 ATAATTTAAT
*
27472328 AAATAA AAATAA AAATCTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
27472369 AATATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:27472369 original size:20 final size:20
Alignment explanation
Indices: 27472331--27472369 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27472321 ATTTAATAAA
**
27472331 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATAAAAAAC
27472351 TAAAAATAAAAATAAAAAA
1 TAAAAATAAAAATAAAAAA
27472370 ATATAATTTT
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:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:27472767 original size:17 final size:17
Alignment explanation
Indices: 27472717--27472767 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
27472707 TAAATGAGCT
27472717 CACACGCCTATGTGGCC
1 CACACGCCTATGTGGCC
* * * *
27472734 TAC-C-CGTGTGGGGCC
1 CACACGCCTATGTGGCC
27472749 CACACGCCTATGTGGCC
1 CACACGCCTATGTGGCC
27472766 CA
1 CA
27472768 TATGGCCCAA
Statistics
Matches: 24, Mismatches: 8, Indels: 4
0.67 0.22 0.11
Matches are distributed among these distances:
15 10 0.42
16 2 0.08
17 12 0.50
ACGTcount: A:0.16, C:0.39, G:0.27, T:0.18
Consensus pattern (17 bp):
CACACGCCTATGTGGCC
Found at i:27475691 original size:21 final size:22
Alignment explanation
Indices: 27475664--27475711 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
27475654 ATATTCATAC
27475664 ATGTGCAAATATCTCATTTATG
1 ATGTGCAAATATCTCATTTATG
27475686 -TGTGCAAATATCTCATTTATG
1 ATGTGCAAATATCTCATTTATG
27475707 ATGTG
1 ATGTG
27475712 GTCTATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (22 bp):
ATGTGCAAATATCTCATTTATG
Found at i:27475746 original size:14 final size:14
Alignment explanation
Indices: 27475727--27475758 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
27475717 TAAATGATTG
27475727 GTGAATAGTTGAAT
1 GTGAATAGTTGAAT
27475741 GTGAATAGTTGAAT
1 GTGAATAGTTGAAT
27475755 GTGA
1 GTGA
27475759 CCTAATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (14 bp):
GTGAATAGTTGAAT
Found at i:27477131 original size:42 final size:42
Alignment explanation
Indices: 27477043--27477182 Score: 131
Period size: 42 Copynumber: 3.4 Consensus size: 42
27477033 ATATTGGCAT
* * * ** *
27477043 GTAAGTGTATCATC-GAATGTACCAAA-AAAACATACCAACAT
1 GTAAGTGCATCATCAG-ATATACCAAAGAAAATATACCGCCAC
* *
27477084 GTAAGTGCATCATCAGATATATCAAAGAAAATATACTGCCAC
1 GTAAGTGCATCATCAGATATACCAAAGAAAATATACCGCCAC
* * * * *
27477126 GTAAGTGCATCATCGGATATACCGAAGAAAATATTCCGGCAT
1 GTAAGTGCATCATCAGATATACCAAAGAAAATATACCGCCAC
*
27477168 GTACGTGCATCATCA
1 GTAAGTGCATCATCA
27477183 AGCATACTGA
Statistics
Matches: 80, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
41 21 0.26
42 59 0.74
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (42 bp):
GTAAGTGCATCATCAGATATACCAAAGAAAATATACCGCCAC
Found at i:27478792 original size:5 final size:5
Alignment explanation
Indices: 27478748--27478777 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
27478738 TTAACTAAAC
27478748 AAAAT AATAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAA
27478778 CCAATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:27479096 original size:3 final size:3
Alignment explanation
Indices: 27479088--27479129 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
27479078 TGTTTGATCC
27479088 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
27479130 GTTGTTGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:27482327 original size:31 final size:31
Alignment explanation
Indices: 27482292--27482352 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
27482282 TTTGGCTGAG
27482292 AGAGAAAGTAAAGTAAAAAGGTAAGAGATTA
1 AGAGAAAGTAAAGTAAAAAGGTAAGAGATTA
27482323 AGAGAAAGTAAAGTAAAAAGGTAAGAGATT
1 AGAGAAAGTAAAGTAAAAAGGTAAGAGATT
27482353 CACACAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.16
Consensus pattern (31 bp):
AGAGAAAGTAAAGTAAAAAGGTAAGAGATTA
Found at i:27486764 original size:35 final size:35
Alignment explanation
Indices: 27486708--27486806 Score: 128
Period size: 35 Copynumber: 2.8 Consensus size: 35
27486698 TGTATGGCCA
* *
27486708 AATACACAAGGTTCATTATATCATCACATATGG-CTG
1 AATATACAA-GTTCAATATATCATCACATATGGTC-G
*
27486744 AATATACAAGTTCAATATATCATCATATATGGTCG
1 AATATACAAGTTCAATATATCATCACATATGGTCG
* *
27486779 AATATACAAGTTCAATAAAACATCACAT
1 AATATACAAGTTCAATATATCATCACAT
27486807 GTAGCCAAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
35 47 0.84
36 9 0.16
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.30
Consensus pattern (35 bp):
AATATACAAGTTCAATATATCATCACATATGGTCG
Found at i:27486820 original size:35 final size:35
Alignment explanation
Indices: 27486744--27486823 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
27486734 CATATGGCTG
* * * * *
27486744 AATATACAAGTTCAATATATCATCATATATGGTCG
1 AATATACAAGTTCAATAAAACATCACATATAGTCC
*
27486779 AATATACAAGTTCAATAAAACATCACATGTAG-CC
1 AATATACAAGTTCAATAAAACATCACATATAGTCC
27486813 AAGTATACAAG
1 AA-TATACAAG
27486824 GTCATTTAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 3 0.08
35 35 0.92
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (35 bp):
AATATACAAGTTCAATAAAACATCACATATAGTCC
Found at i:27488553 original size:12 final size:13
Alignment explanation
Indices: 27488524--27488561 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
27488514 AATATATTGT
*
27488524 TTTTAATTTTTAA
1 TTTTAATTTATAA
27488537 TTTTAATTTAT-A
1 TTTTAATTTATAA
*
27488549 TTTTAATTAATAA
1 TTTTAATTTATAA
27488562 ATATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTAATTTATAA
Found at i:27500461 original size:23 final size:24
Alignment explanation
Indices: 27500435--27500481 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27500425 AAAAGATAAT
*
27500435 AGAAAAT-GAAGAAAAAAATTAAA
1 AGAAAATAAAAGAAAAAAATTAAA
*
27500458 AGAATATAAAAGAAAAAAATTAAA
1 AGAAAATAAAAGAAAAAAATTAAA
27500482 TTGCTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (24 bp):
AGAAAATAAAAGAAAAAAATTAAA
Found at i:27501349 original size:84 final size:84
Alignment explanation
Indices: 27501208--27501375 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
27501198 GCCAACAAAC
27501208 CCGCCCCGGTTTACCAAGAAGTGAGTGAAATCCTCGATTCTCTTTCATGGGTTTAGTTAAAAATG
1 CCGCCCCGGTTTACCAAGAAGTGAGTGAAATCCTCGATTCTCTTTCATGGGTTTAGTTAAAAATG
27501273 GGGGCATTTATCTTACCTT
66 GGGGCATTTATCTTACCTT
27501292 CCGCCCCGGTTTACCAAGAAGTGAGTGAAATCCTCGATTCTCTTTCATGGGTTTAGTTAAAAATG
1 CCGCCCCGGTTTACCAAGAAGTGAGTGAAATCCTCGATTCTCTTTCATGGGTTTAGTTAAAAATG
27501357 GGGGCATTTATCTTACCTT
66 GGGGCATTTATCTTACCTT
27501376 GATCTCTTTG
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (84 bp):
CCGCCCCGGTTTACCAAGAAGTGAGTGAAATCCTCGATTCTCTTTCATGGGTTTAGTTAAAAATG
GGGGCATTTATCTTACCTT
Found at i:27505385 original size:146 final size:147
Alignment explanation
Indices: 27505064--27505412 Score: 411
Period size: 146 Copynumber: 2.4 Consensus size: 147
27505054 ATTGTGGTAC
* * * *
27505064 ACCAAAATTTCTAAGCGCAAATCCTTAGATATTTTGGTATAT-TCTATAATTTCTAAGGGAATAC
1 ACCAAAATTTCTAAGAGCAAATCCTTAGATATTTTGGTATATACCT-CAATTTCTAAAGGAATAC
* * * **
27505128 TAATATTTTTATAGAATCTCGTAAGAAATTTTGGTATACCAAAATCATGTTGTACAAGCCTATAA
65 TAATATTTCTATAGAACCTCGTAAGAAATTTTGATATACCAAAATCAAATTGTACAAGCCTATAA
*
27505193 CAAGATTTCTAATGAAAT
130 CAAGATTTCTAATAAAAT
* *** *
27505211 ACCAAAATTTTTAAGAGGTTATCTTTAGATATTTTGGTATATACCTCAATTTCTAAAGGAATA-T
1 ACCAAAATTTCTAAGAGCAAATCCTTAGATATTTTGGTATATACCTCAATTTCTAAAGGAATACT
* *
27505275 CAATATTTCTATGGAACCTCGTTAG-AATTTTGATATACCAAAATCTAAATT-TACAAGCCTATA
66 -AATATTTCTATAGAACCTCGTAAGAAATTTTGATATACCAAAATC-AAATTGTACAAGCCTATA
*
27505338 CCAAGATTTCTAATAAAAT
129 ACAAGATTTCTAATAAAAT
* ** * * *
27505357 ATCACTATTTCTAATAGCACATCCTTAGATATTTTAGTATATACC-CAAATTTCTAA
1 ACCAAAATTTCTAAGAGCAAATCCTTAGATATTTTGGTATATACCTC-AATTTCTAA
27505413 CAAGGTGGTA
Statistics
Matches: 170, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
145 1 0.01
146 93 0.55
147 74 0.44
148 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (147 bp):
ACCAAAATTTCTAAGAGCAAATCCTTAGATATTTTGGTATATACCTCAATTTCTAAAGGAATACT
AATATTTCTATAGAACCTCGTAAGAAATTTTGATATACCAAAATCAAATTGTACAAGCCTATAAC
AAGATTTCTAATAAAAT
Found at i:27509720 original size:23 final size:23
Alignment explanation
Indices: 27509690--27509736 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
27509680 TACTAAATTC
*
27509690 CCAAATAATGCGTTGAATCATGT
1 CCAAATAATGCATTGAATCATGT
27509713 CCAAATAATGCATTGAATCATGT
1 CCAAATAATGCATTGAATCATGT
27509736 C
1 C
27509737 TACAAGTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (23 bp):
CCAAATAATGCATTGAATCATGT
Found at i:27519905 original size:28 final size:29
Alignment explanation
Indices: 27519840--27519924 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 29
27519830 GAAAATAAAC
*
27519840 CTAACTTATTAAAAATTCCTAAATATAAATT
1 CTAACTTATT-AAAA-CCCTAAATATAAATT
*
27519871 -TATCTTATTAAAACCCTAAATAT-AATT
1 CTAACTTATTAAAACCCTAAATATAAATT
* *
27519898 CTAACTTA-TAAGAACCTTAAATCTAAA
1 CTAACTTATTAA-AACCCTAAATATAAA
27519925 AAATAAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
27 7 0.15
28 25 0.54
29 6 0.13
30 8 0.17
ACGTcount: A:0.47, C:0.15, G:0.01, T:0.36
Consensus pattern (29 bp):
CTAACTTATTAAAACCCTAAATATAAATT
Found at i:27528512 original size:30 final size:28
Alignment explanation
Indices: 27528478--27528542 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
27528468 AATTCCCACA
27528478 AAAAAAAAAGAAAAGAAAAAGGAAAAATTG
1 AAAAAAAAAGAAAAGAAAAA--AAAAATTG
** * *
27528508 AAAAATCAAGAAAAGATAAAAAAAATTT
1 AAAAAAAAAGAAAAGAAAAAAAAAATTG
27528536 AAAAAAA
1 AAAAAAA
27528543 TATTTTTTGG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
28 12 0.41
30 17 0.59
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.11
Consensus pattern (28 bp):
AAAAAAAAAGAAAAGAAAAAAAAAATTG
Found at i:27529190 original size:149 final size:151
Alignment explanation
Indices: 27528873--27529179 Score: 537
Period size: 149 Copynumber: 2.0 Consensus size: 151
27528863 TGGCTTCTTA
27528873 GAGCCTTAGGTCAACTTTGTTAGAAAGTGATCCCACATCTTTTTCGAATATTATTGAGTTTGATT
1 GAGCCTTAGGTCAACTTTGTTAGAAAGTGATCCCACATCTTTTTCGAATATTATTGAGTTTGATT
* *
27528938 ACTCTTTAAAAGTTACAAGTGAGAAAATCTTAACTTCTTTTCTTTGTCTTCTAGAGTTGTTTATT
66 ACTCTTTAAAAGTTACAAGTGAGAAAATCTTAACTTCTTTTCCTTGTCTCCTAGAGTTGTTTATT
27529003 TTATTGCAAGTGCATAACGAC
131 TTATTGCAAGTGCATAACGAC
*
27529024 GAGCCTTAGGTCAACTTTGTTAGAAAGTGATCCCATATC-TTTTCGAATATTATTGAGTTTGATT
1 GAGCCTTAGGTCAACTTTGTTAGAAAGTGATCCCACATCTTTTTCGAATATTATTGAGTTTGATT
27529088 ACTCTTTAAAAGTTACAAGTGAG-AAATCTTAACTTCTTTTCCTTGTCTCCTAGAGTTGTTTATT
66 ACTCTTTAAAAGTTACAAGTGAGAAAATCTTAACTTCTTTTCCTTGTCTCCTAGAGTTGTTTATT
** * *
27529152 TTATTGTGAGTGCATAATGGC
131 TTATTGCAAGTGCATAACGAC
27529173 GAGCCTT
1 GAGCCTT
27529180 GGTTTTACTT
Statistics
Matches: 149, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
149 63 0.42
150 48 0.32
151 38 0.26
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (151 bp):
GAGCCTTAGGTCAACTTTGTTAGAAAGTGATCCCACATCTTTTTCGAATATTATTGAGTTTGATT
ACTCTTTAAAAGTTACAAGTGAGAAAATCTTAACTTCTTTTCCTTGTCTCCTAGAGTTGTTTATT
TTATTGCAAGTGCATAACGAC
Found at i:27531810 original size:6 final size:6
Alignment explanation
Indices: 27531799--27531828 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
27531789 TAGGTTTCCA
27531799 AAAATG AAAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG
27531829 GAAGCTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:27532009 original size:26 final size:26
Alignment explanation
Indices: 27531975--27532062 Score: 151
Period size: 26 Copynumber: 3.4 Consensus size: 26
27531965 GAATTTTCTT
*
27531975 AAAATTTTACCAGGGGTAAAAAT-GTT
1 AAAATTTTACCAGGGGT-AAAATCGTC
27532001 AAAATTTTACCAGGGGTAAAATCGTC
1 AAAATTTTACCAGGGGTAAAATCGTC
27532027 AAAATTTTACCAGGGGTAAAATCGTC
1 AAAATTTTACCAGGGGTAAAATCGTC
27532053 AAAATTTTAC
1 AAAATTTTAC
27532063 TAGGCTAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
25 5 0.08
26 55 0.92
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (26 bp):
AAAATTTTACCAGGGGTAAAATCGTC
Found at i:27532563 original size:53 final size:53
Alignment explanation
Indices: 27532502--27532608 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
27532492 CCCTAAAAGG
*
27532502 AATGTTTTTTCTAGTTTTGTGTTTTGATTTAATTGGTTCGAACCCATACTTGA
1 AATGTTTTTTCTAGTTCTGTGTTTTGATTTAATTGGTTCGAACCCATACTTGA
27532555 AATGTTTTTTCTAGTTCTGTGTTTTGATTTAATTGGTTCGAACCCATACTTGA
1 AATGTTTTTTCTAGTTCTGTGTTTTGATTTAATTGGTTCGAACCCATACTTGA
27532608 A
1 A
27532609 GCAGTTTGTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (53 bp):
AATGTTTTTTCTAGTTCTGTGTTTTGATTTAATTGGTTCGAACCCATACTTGA
Found at i:27535093 original size:28 final size:30
Alignment explanation
Indices: 27535042--27535105 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
27535032 ACGGGCTGGG
27535042 CACACAGTTGTGTGAGCCCACACAGGCTGC
1 CACACAGTTGTGTGAGCCCACACAGGCTGC
*
27535072 CACACGGTTGTGTGAGCCCACACAGGCTGC
1 CACACAGTTGTGTGAGCCCACACAGGCTGC
27535102 CACA
1 CACA
27535106 GTCATGTGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.34, G:0.27, T:0.16
Consensus pattern (30 bp):
CACACAGTTGTGTGAGCCCACACAGGCTGC
Found at i:27536224 original size:15 final size:13
Alignment explanation
Indices: 27536184--27536230 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 13
27536174 AATTTAGCCA
27536184 TTTTTATATTTATAT
1 TTTTTA-ATTTA-AT
27536199 TTTTTAATTTAAT
1 TTTTTAATTTAAT
27536212 TTTTTACATTTTAAT
1 TTTTTA-A-TTTAAT
27536227 TTTT
1 TTTT
27536231 CATTTGTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.27
14 6 0.20
15 16 0.53
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:27536654 original size:20 final size:20
Alignment explanation
Indices: 27536622--27536661 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27536612 CCAAATACTC
*
27536622 ATTTGGCTAACTTTTTAGAT
1 ATTTGGCTAACTTTTAAGAT
27536642 ATTT-GCTACACTTTTAAGAT
1 ATTTGGCTA-ACTTTTAAGAT
27536662 TAATGGCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
ATTTGGCTAACTTTTAAGAT
Found at i:27545362 original size:39 final size:39
Alignment explanation
Indices: 27545308--27545632 Score: 426
Period size: 39 Copynumber: 8.3 Consensus size: 39
27545298 TAATGGAGAA
*
27545308 TTATATCCGGGCTAAGTCCAGAAGGCATTCGTGCGGGTG
1 TTATATCCGGGCTAAGTCCAGAAGGCATTCGTGCTGGTG
27545347 TTATATCCGGGCTAAGTCCCA-AAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGT-CCAGAAGGCATTCGTGCTGGTG
27545386 TTATATCCGGGCTAAGTCCCA-AAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGT-CCAGAAGGCATTCGTGCTGGTG
27545425 TTATATCCGGGCTAAGTCCCA-AAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGT-CCAGAAGGCATTCGTGCTGGTG
* * * *
27545464 TTATATCCAGGTTAAGCCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCAGAAGGCATTCGTGCTGGTG
* * *
27545503 TTATATCCGGGTTAAGCCCAGAAGGCATTTGTGCTGGTG
1 TTATATCCGGGCTAAGTCCAGAAGGCATTCGTGCTGGTG
* * * *
27545542 TTATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCAGAAGGCATTCGTGCTGGTG
* * * *
27545581 TTATATCCGGGCTAAAGTCCTGCAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCAGAAGGCATTCGTGCTGGTG
27545620 TTATATCCGGGCT
1 TTATATCCGGGCT
27545633 TAAAGTCCCG
Statistics
Matches: 269, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
38 2 0.01
39 254 0.94
40 13 0.05
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.30
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCAGAAGGCATTCGTGCTGGTG
Found at i:27549735 original size:51 final size:51
Alignment explanation
Indices: 27549650--27549774 Score: 146
Period size: 51 Copynumber: 2.5 Consensus size: 51
27549640 CGGATACTCG
* *
27549650 GTGGCCTGCACATAGTACCACCCTTGTAGTCAAAGCTACCTTCTT-CAAAAA
1 GTGGCCTGCACATAGTACCACACTTGTAGTCAAAGCTACATT-TTACAAAAA
* * * * *
27549701 GTGGCCTTCACATAGTACCACATTTGT-GTCCAAAGCTATATTTTACACATA
1 GTGGCCTGCACATAGTACCACACTTGTAGT-CAAAGCTACATTTTACAAAAA
*
27549752 GTGGCCTGCACTTAGTACCACAC
1 GTGGCCTGCACATAGTACCACAC
27549775 ATGTGATCGA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
50 4 0.06
51 58 0.94
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (51 bp):
GTGGCCTGCACATAGTACCACACTTGTAGTCAAAGCTACATTTTACAAAAA
Found at i:27549788 original size:51 final size:51
Alignment explanation
Indices: 27549704--27549881 Score: 153
Period size: 51 Copynumber: 3.5 Consensus size: 51
27549694 TCAAAAAGTG
* * ** * ** *
27549704 GCCTTCACATAGTACCACATTTGTG-TCCAAAGCTATATTTTACACATAGTG
1 GCCTGCACTTAGTACCACACATGTGAT-CAAAGCTATCTGGTACACATAGTA
* * *
27549755 GCCTGCACTTAGTACCACACATGTGATCGAAGCTATCGGGTACGCATAGTA
1 GCCTGCACTTAGTACCACACATGTGATCAAAGCTATCTGGTACACATAGTA
** * * * * *
27549806 GCCTGCACTTAGTATTACACATGCGACCTAA-CCATCTGGTACACGTAGTA
1 GCCTGCACTTAGTACCACACATGTGATCAAAGCTATCTGGTACACATAGTA
* *
27549856 GCCTGCACTTAGTACTACACACGTGA
1 GCCTGCACTTAGTACCACACATGTGA
27549882 CCTAAAACCA
Statistics
Matches: 103, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
50 38 0.37
51 64 0.62
52 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (51 bp):
GCCTGCACTTAGTACCACACATGTGATCAAAGCTATCTGGTACACATAGTA
Found at i:27549866 original size:50 final size:51
Alignment explanation
Indices: 27549744--27549886 Score: 180
Period size: 50 Copynumber: 2.8 Consensus size: 51
27549734 AGCTATATTT
* * * * *
27549744 TACACATAGTGGCCTGCACTTAGTACCACACATGTGATCGAAGCTATCGGG
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCCATCGGG
* * * *
27549795 TACGCATAGTAGCCTGCACTTAGTATTACACATGCGACCTAA-CCATCTGG
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCCATCGGG
* *
27549845 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
27549887 AACCATTTTA
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 43 0.55
51 35 0.45
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (51 bp):
TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCCATCGGG
Found at i:27549913 original size:52 final size:50
Alignment explanation
Indices: 27549745--27549915 Score: 144
Period size: 50 Copynumber: 3.4 Consensus size: 50
27549735 GCTATATTTT
* * * * * * * * **
27549745 ACACATAGTGGCCTGCACTTAGTACCACACATGTGATCGAAGCTATCGGGT
1 ACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTAA-CCATCTGAA
* * * **
27549796 ACGCATAGTAGCCTGCACTTAGTATTACACATGCGACCTAACCATCTGGT
1 ACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCTGAA
* * * *
27549846 ACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAAACCATTTTAA
1 ACACATAGTAGCCTGCACTTAGTACTACACACGCGACCT--AACCATCTGAA
27549898 ACACATAGTAGCCTGCAC
1 ACACATAGTAGCCTGCAC
27549916 ATGTGTTCTC
Statistics
Matches: 99, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
50 41 0.41
51 34 0.34
52 24 0.24
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (50 bp):
ACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCTGAA
Done.