Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 56 of 163
Found at i:18191219 original size:17 final size:17
Alignment explanation
Indices: 18191193--18191226 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18191183 TTCCCTGGCC
*
18191193 CAAATCAAATAAATAAA
1 CAAATAAAATAAATAAA
18191210 CAAATAAAATAAATAAA
1 CAAATAAAATAAATAAA
18191227 TAAAACCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (17 bp):
CAAATAAAATAAATAAA
Found at i:18191221 original size:13 final size:13
Alignment explanation
Indices: 18191198--18191231 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
18191188 TGGCCCAAAT
18191198 CAAAT-AAATAAA
1 CAAATAAAATAAA
18191210 CAAATAAAATAAA
1 CAAATAAAATAAA
*
18191223 TAAATAAAA
1 CAAATAAAA
18191232 CCAAGTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (13 bp):
CAAATAAAATAAA
Found at i:18200337 original size:11 final size:11
Alignment explanation
Indices: 18200321--18200346 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18200311 TTGCTTTAAT
18200321 TGCTATCTTTA
1 TGCTATCTTTA
18200332 TGCTATCTTTA
1 TGCTATCTTTA
18200343 TGCT
1 TGCT
18200347 TTATTGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.19, G:0.12, T:0.54
Consensus pattern (11 bp):
TGCTATCTTTA
Found at i:18202087 original size:25 final size:25
Alignment explanation
Indices: 18201999--18202088 Score: 67
Period size: 25 Copynumber: 3.6 Consensus size: 25
18201989 TCATGTACAT
* * *
18201999 GTATGCTCATACGAGCTGTGAATTG
1 GTATGATCATACGAGCTATAAATTG
* * * * *
18202024 GTATGGTCACT-TGAACTATAGATCG
1 GTATGATCA-TACGAGCTATAAATTG
*
18202049 GTATGTTC-TCACGAGCTATAAATTG
1 GTATGATCAT-ACGAGCTATAAATTG
18202074 GTATGATCATACGAG
1 GTATGATCATACGAG
18202089 TTGTAGGTCG
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
23 1 0.02
25 45 0.94
26 2 0.04
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (25 bp):
GTATGATCATACGAGCTATAAATTG
Found at i:18207421 original size:17 final size:17
Alignment explanation
Indices: 18207366--18207420 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
18207356 TCTAATTGCC
18207366 AATTGATACCTTTAACT
1 AATTGATACCTTTAACT
*
18207383 AATTGA-A-CTTCATAGCT
1 AATTGATACCTT--TAACT
*
18207400 AATTTATACCTTTAACT
1 AATTGATACCTTTAACT
18207417 AATT
1 AATT
18207421 TTATGTCCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 3 0.10
16 1 0.03
17 23 0.74
18 1 0.03
19 3 0.10
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42
Consensus pattern (17 bp):
AATTGATACCTTTAACT
Found at i:18221626 original size:12 final size:12
Alignment explanation
Indices: 18221609--18221636 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18221599 TTACATGCCC
18221609 GTGTGTTAGGCT
1 GTGTGTTAGGCT
18221621 GTGTGTTAGGCT
1 GTGTGTTAGGCT
18221633 GTGT
1 GTGT
18221637 AAATTCCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.43, T:0.43
Consensus pattern (12 bp):
GTGTGTTAGGCT
Found at i:18225434 original size:29 final size:29
Alignment explanation
Indices: 18225402--18225645 Score: 267
Period size: 29 Copynumber: 8.4 Consensus size: 29
18225392 CTTCGTCACC
18225402 ATCCCTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
* *
18225431 ATCCCTTTTAATAATCGATTGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
18225460 ATCCCTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
* * * * *
18225489 ATCCCTTTTTATATTCGATGGTCGTCA-CT
1 ATCCCTTTTCATAATCGATAGCCG-AAGCT
* * * * * * *
18225518 GTCCCTTTTCATAGTTGATGGTCGTCA-CC
1 ATCCCTTTTCATAATCGATAGCCG-AAGCT
*
18225547 ATCCCTTTTCATAATCGATAGCCAAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
* * *
18225576 ATCCCTTTTCATATTCGATAACTGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
* *
18225605 ATCCCTTTTCATATTCGATACCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
*
18225634 ATCCTTTTTCAT
1 ATCCCTTTTCAT
18225646 TGGTCAATGA
Statistics
Matches: 184, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
28 1 0.01
29 182 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCGAAGCT
Found at i:18233516 original size:23 final size:23
Alignment explanation
Indices: 18233481--18233562 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
18233471 AGTGTTATTG
* *
18233481 ATCAATGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
18233504 CTCAGTGGTAGCTACGACTACAT
1 ATCAGTGGTAGCTACGGCTACAT
*
18233527 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
18233550 ATCAGTGGTAGCT
1 ATCAGTGGTAGCT
18233563 TCGTTAGGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:18233593 original size:16 final size:17
Alignment explanation
Indices: 18233572--18233605 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18233562 TTCGTTAGGG
*
18233572 GCAAAAGT-TTAATTTT
1 GCAAAAGTATGAATTTT
18233588 GCAAAAGTATGAATTTT
1 GCAAAAGTATGAATTTT
18233605 G
1 G
18233606 GACTAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (17 bp):
GCAAAAGTATGAATTTT
Found at i:18234821 original size:219 final size:219
Alignment explanation
Indices: 18234436--18234866 Score: 639
Period size: 219 Copynumber: 2.0 Consensus size: 219
18234426 CATTGAAATG
*
18234436 TTAAGTTATATTCATGATTTACGTACATACTAAGCATTATATGCTTACACAGTCTTCTTTCTCAT
1 TTAAGTTATATTCATGATTTACGAACATACTAAGCATTATATGCTTACACAGTCTTCTTTCTCAT
* * * * *
18234501 TTTTTTTATAATCGGAAGCTCAATCGGTTTGGAAGTTTGTCGAAGATCTATCACACTATCCAGTG
66 GTTTTTTATAATAGGAAGCTCAATCAGTTTGGAAGCTCGTCGAAGATCTATCACACTATCCAGTG
* * * *
18234566 AATATATTGTTAGGTTTTTATGTTTTGGCTAAGGTTATAATGGCATGTATAGGTGGACTTGTGTT
131 AATACATTGGTAGGTTTTTATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTATGTT
*
18234631 TAATGGTCTTGTTGATAGGTGGAC
196 TAATGCTCTTGTTGATAGGTGGAC
* * ** * *
18234655 TTAAGTTATATTCATGATTTACGAACTTACTAATCATTATATGCTTACGTAGTTTTCTTTTTCAT
1 TTAAGTTATATTCATGATTTACGAACATACTAAGCATTATATGCTTACACAGTCTTCTTTCTCAT
* * * * *
18234720 GTTTTTTATAATAGGAAGCTCGATTAGTTTTGACGCTCGTCGGAGATCTATCACACTATCCAGTG
66 GTTTTTTATAATAGGAAGCTCAATCAGTTTGGAAGCTCGTCGAAGATCTATCACACTATCCAGTG
*
18234785 AATACATTGGTA-GTTTTTGATGTTTTGGCCAAGGTTATAATGGCTTGTATAGGTGGACTTATGT
131 AATACATTGGTAGGTTTTT-ATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTATGT
18234849 TTAATGCTCTTGTTGATA
195 TTAATGCTCTTGTTGATA
18234867 TGGTTAGCAT
Statistics
Matches: 188, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
218 6 0.03
219 182 0.97
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (219 bp):
TTAAGTTATATTCATGATTTACGAACATACTAAGCATTATATGCTTACACAGTCTTCTTTCTCAT
GTTTTTTATAATAGGAAGCTCAATCAGTTTGGAAGCTCGTCGAAGATCTATCACACTATCCAGTG
AATACATTGGTAGGTTTTTATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTATGTT
TAATGCTCTTGTTGATAGGTGGAC
Found at i:18240393 original size:15 final size:15
Alignment explanation
Indices: 18240373--18240406 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18240363 AAAAGTGTCA
18240373 TCTTCTTCAAACTG-T
1 TCTTCTTC-AACTGAT
18240388 TCTTCTTCAACTGAT
1 TCTTCTTCAACTGAT
18240403 TCTT
1 TCTT
18240407 TAAGAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.18, C:0.26, G:0.06, T:0.50
Consensus pattern (15 bp):
TCTTCTTCAACTGAT
Found at i:18242107 original size:220 final size:220
Alignment explanation
Indices: 18241704--18242128 Score: 649
Period size: 220 Copynumber: 1.9 Consensus size: 220
18241694 ATTGAAATGG
*
18241704 TAAGTTATATTCATAATTTACGAACTTACCAAGCATTATATGCTTACGTAGTTTTCTTTCTCATG
1 TAAGTTATATGCATAATTTACGAACTTACCAAGCATTATATGCTTACGTAGTTTTCTTTCTCATG
* * **
18241769 TTTTTTTAAAATCAGAAGCTCGATAGGTTTGGAAGCTTGTTGGAGATCTATCACACTATCCAACG
66 TTTTTTCAAAATCAGAAGCTCGATAGGTTTGGAAGCTCGTCAGAGATCTATCACACTATCCAACG
*
18241834 AATATATCGATAGTTTTTTATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTTTATT
131 AATATATCGATAGTTTTTTATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTGTATT
18241899 TAATGATCTTCTTTATAGGTGGAAT
196 TAATGATCTTCTTTATAGGTGGAAT
* * * *
18241924 TAAGTTGTATGCATGATTTATGAACTTACTAAGCATTATATGCTTACGTAGTTTTCTTTCGT-AT
1 TAAGTTATATGCATAATTTACGAACTTACCAAGCATTATATGCTTACGTAGTTTTCTTTC-TCAT
* * *
18241988 -TTTTTTCATAATCGGAAGCTCGATCA-GTTTGGAAGCTCGTCAGAGATCTATCACACTATCCAG
65 GTTTTTTCAAAATCAGAAGCTCGAT-AGGTTTGGAAGCTCGTCAGAGATCTATCACACTATCCAA
* * *
18242051 CGAATATATGGGTAGTTTTTTTATGTTTTGGCCAAGGTTATAGTGGCATGTATAGGTGGACTTGT
129 CGAATATATCGATAG-TTTTTTATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTGT
*
18242116 GTTTAATGATCTT
193 ATTTAATGATCTT
18242129 GTTGATATGG
Statistics
Matches: 185, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
219 67 0.36
220 117 0.63
221 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (220 bp):
TAAGTTATATGCATAATTTACGAACTTACCAAGCATTATATGCTTACGTAGTTTTCTTTCTCATG
TTTTTTCAAAATCAGAAGCTCGATAGGTTTGGAAGCTCGTCAGAGATCTATCACACTATCCAACG
AATATATCGATAGTTTTTTATGTTTTGGCCAAGGTTATAATGGCATGTATAGGTGGACTTGTATT
TAATGATCTTCTTTATAGGTGGAAT
Found at i:18247044 original size:107 final size:107
Alignment explanation
Indices: 18246916--18247129 Score: 410
Period size: 107 Copynumber: 2.0 Consensus size: 107
18246906 AAATATCTCA
*
18246916 AAATATATAACTTCTTTTGTTGCTCTATTTCTTTTATGTAAAAATATACTCATTAAGCTTTCATT
1 AAATATATAACTTCTTTTGTTGCTCTATTTCTTTTATGTAAAAATATACTCATTAAGCTTTCAGT
*
18246981 TCATATTTTATTCACTCTGTAATTCAATTTCCATCATTTTTG
66 TCATATTTTATTCACTCTCTAATTCAATTTCCATCATTTTTG
18247023 AAATATATAACTTCTTTTGTTGCTCTATTTCTTTTATGTAAAAATATACTCATTAAGCTTTCAGT
1 AAATATATAACTTCTTTTGTTGCTCTATTTCTTTTATGTAAAAATATACTCATTAAGCTTTCAGT
18247088 TCATATTTTATTCACTCTCTAATTCAATTTCCATCATTTTTG
66 TCATATTTTATTCACTCTCTAATTCAATTTCCATCATTTTTG
18247130 GTGATTTTTC
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (107 bp):
AAATATATAACTTCTTTTGTTGCTCTATTTCTTTTATGTAAAAATATACTCATTAAGCTTTCAGT
TCATATTTTATTCACTCTCTAATTCAATTTCCATCATTTTTG
Found at i:18247201 original size:16 final size:16
Alignment explanation
Indices: 18247180--18247211 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18247170 ATTTTGTTGC
*
18247180 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
18247196 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
18247212 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:18256578 original size:49 final size:49
Alignment explanation
Indices: 18256501--18256600 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
18256491 TCCTATAGAG
* ** * *
18256501 AACATATGAAAAGCATTAAACATGTTATATTCTTTCCAAAAGGAATTAT
1 AACATATGAAAAGCATTAAAAAAATTATATTATTTCCAAAAAGAATTAT
* *
18256550 AACATATGAAAAGTATTAAAAAAATTATATTATTTCCAAAAATAATTAT
1 AACATATGAAAAGCATTAAAAAAATTATATTATTTCCAAAAAGAATTAT
18256599 AA
1 AA
18256601 ATGTTTCAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (49 bp):
AACATATGAAAAGCATTAAAAAAATTATATTATTTCCAAAAAGAATTAT
Found at i:18258971 original size:42 final size:42
Alignment explanation
Indices: 18258925--18259026 Score: 100
Period size: 42 Copynumber: 2.5 Consensus size: 42
18258915 GTCACACGGT
* **
18258925 CGTGTACCTTAGTCACA-AGGGTGTGTCCCTCAGCCACACAAC
1 CGTGTACCTTACTCACACA-GGCATGTCCCTCAGCCACACAAC
* * * **
18258967 CGTGTATCTCACTCACACAGGCATGTCCCTCAGTCACACGGC
1 CGTGTACCTTACTCACACAGGCATGTCCCTCAGCCACACAAC
*
18259009 CGTGTACCTTGC-CACACA
1 CGTGTACCTTACTCACACA
18259027 CTCTGGGCCT
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 6 0.12
42 41 0.85
43 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.22
Consensus pattern (42 bp):
CGTGTACCTTACTCACACAGGCATGTCCCTCAGCCACACAAC
Found at i:18260894 original size:39 final size:39
Alignment explanation
Indices: 18260839--18260940 Score: 141
Period size: 39 Copynumber: 2.6 Consensus size: 39
18260829 AACATGTTTT
*
18260839 TGAGTATTGTGATATATGGTTAAATGTTATGTCATTACA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTCATTACA
* * * *
18260878 TGAGTATTGTGCTATATACTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTCATTACA
* *
18260917 TGTGTAATGTGATATATGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
18260941 AGTGAATATG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTCATTACA
Found at i:18262155 original size:33 final size:33
Alignment explanation
Indices: 18262113--18262178 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
18262103 GATCCTTAAG
18262113 ATTGTTCGAAAGGGATTTTTTAGGATAAACATT
1 ATTGTTCGAAAGGGATTTTTTAGGATAAACATT
*
18262146 ATTGTTCGAAAGTGATTTTTTAGGATAAACATT
1 ATTGTTCGAAAGGGATTTTTTAGGATAAACATT
18262179 GTTTGGTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (33 bp):
ATTGTTCGAAAGGGATTTTTTAGGATAAACATT
Found at i:18263384 original size:42 final size:42
Alignment explanation
Indices: 18263295--18263396 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 42
18263285 CTCACACGGC
* * *
18263295 CGTGTACCTTAGTCACATGGGCATGTCCTTAAGCCACACAGT
1 CGTGTACCTTAGTCACACGGGCATGCCCTTAAGCCACACAGA
* * **
18263337 TGTGTATCTTAGTCACACGGGCATGCCCCTT-AGCCACATGGA
1 CGTGTACCTTAGTCACACGGGCATG-CCCTTAAGCCACACAGA
*
18263379 CGTGTACCCTA-TCACACG
1 CGTGTACCTTAGTCACACG
18263397 ATCTTGACCT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 7 0.14
42 38 0.78
43 4 0.08
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (42 bp):
CGTGTACCTTAGTCACACGGGCATGCCCTTAAGCCACACAGA
Found at i:18268121 original size:16 final size:16
Alignment explanation
Indices: 18268090--18268126 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
18268080 ATATGTAGAA
18268090 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
18268106 TATT-TTTAAAAGTTAT
1 TATTATTTAAAA-TTAT
18268122 TATTA
1 TATTA
18268127 AATAAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:18268632 original size:42 final size:42
Alignment explanation
Indices: 18268543--18268644 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 42
18268533 CTCACACGGC
* * *
18268543 CGTGTACCTTAGTCACATGGGCATGTCCTTAAGCCACACAGT
1 CGTGTACCTTAGTCACACGGGCATGCCCTTAAGCCACACAGA
* * **
18268585 TGTGTATCTTAGTCACACGGGCATGCCCCTT-AGCCACATGGA
1 CGTGTACCTTAGTCACACGGGCATG-CCCTTAAGCCACACAGA
*
18268627 CGTGTACCCTA-TCACACG
1 CGTGTACCTTAGTCACACG
18268645 ATCTTGACCT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 7 0.14
42 38 0.78
43 4 0.08
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (42 bp):
CGTGTACCTTAGTCACACGGGCATGCCCTTAAGCCACACAGA
Found at i:18273369 original size:16 final size:16
Alignment explanation
Indices: 18273338--18273374 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
18273328 ATATGTAGAA
18273338 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
18273354 TATT-TTTAAAAGTTAT
1 TATTATTTAAAA-TTAT
18273370 TATTA
1 TATTA
18273375 AATAAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:18278902 original size:18 final size:20
Alignment explanation
Indices: 18278861--18278907 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
18278851 ATATGTGTAC
18278861 ATATATAAGGTATATAAATA
1 ATATATAAGGTATATAAATA
18278881 ATATATAA-GTATGA-AAATA
1 ATATATAAGGTAT-ATAAATA
18278900 TATATATA
1 -ATATATA
18278908 CAAATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (20 bp):
ATATATAAGGTATATAAATA
Found at i:18278960 original size:24 final size:23
Alignment explanation
Indices: 18278927--18278972 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
18278917 TTAAAAAAAT
* *
18278927 ATGTACGTATGTATATATGACAAA
1 ATGTAAGTATGTACATAT-ACAAA
18278951 ATGTAAGTATGTACATATACAA
1 ATGTAAGTATGTACATATACAA
18278973 CAAAATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (23 bp):
ATGTAAGTATGTACATATACAAA
Found at i:18279046 original size:18 final size:18
Alignment explanation
Indices: 18278995--18279052 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
18278985 CTAAAATGAC
18278995 ATAAATAGGTAAATCATA
1 ATAAATAGGTAAATCATA
* * *
18279013 A-CAATA-AT-AATAATA
1 ATAAATAGGTAAATCATA
18279028 ATAAATAGGTAAATCATA
1 ATAAATAGGTAAATCATA
*
18279046 ACAAATA
1 ATAAATA
18279053 AAGGATTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
15 7 0.23
16 5 0.17
17 5 0.17
18 13 0.43
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (18 bp):
ATAAATAGGTAAATCATA
Found at i:18283222 original size:50 final size:50
Alignment explanation
Indices: 18283098--18283474 Score: 406
Period size: 50 Copynumber: 7.6 Consensus size: 50
18283088 GATAATAACA
* * ** * * *
18283098 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCCTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * ** *
18283147 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *** *
18283197 TGTCC-ATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCCCGG
1 TG-CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
18283247 TGCCAACGCCATGTCCCAAACACGATGTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
18283297 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
18283347 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
18283397 TGCCAACGCTATGTCCCAGACATGGTCTTACACT-GG--CTCACATATCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCGG
* * *
18283445 TGTCGATGCCATGTCCCAGACATGGTCTTA
1 TGCCAACGCCATGTCCCAGACATGGTCTTA
18283475 TATGAGATCG
Statistics
Matches: 280, Mismatches: 43, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
48 36 0.13
49 39 0.14
50 202 0.72
51 3 0.01
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:18286906 original size:43 final size:44
Alignment explanation
Indices: 18286698--18286927 Score: 197
Period size: 43 Copynumber: 5.3 Consensus size: 44
18286688 CTAAGATAAC
**
18286698 TGTATTGGAATCACCATTCATTTGCATTTGCAAAATCTTAGTAT
1 TGTATTGGAATCATTATTCATTTGCATTTGCAAAATCTTAGTAT
* * * * *
18286742 CGTATT-GAA--ATTA-TCA-TT-CCTTTGCAACATTTTAGTTT
1 TGTATTGGAATCATTATTCATTTGCATTTGCAAAATCTTAGTAT
* * *
18286780 TGTATTGGAATCATTATGGT-AATTGTATTGGTTGGAAAATCTTAGTAT
1 TGTATTGGAATCATTAT--TCATTTGCA-T--TTGCAAAATCTTAGTAT
* **
18286828 TGTAATGGAATCACCATTCATTTGCATTTGCAAAATCTTAGTAT
1 TGTATTGGAATCATTATTCATTTGCATTTGCAAAATCTTAGTAT
** * *
18286872 TGTATTGGAAT-ATTATTCATTTGTGTTTGTAAAATCTTAGTAC
1 TGTATTGGAATCATTATTCATTTGCATTTGCAAAATCTTAGTAT
*
18286915 TGTATCGGAATCA
1 TGTATTGGAATCA
18286928 CTATGGTAAT
Statistics
Matches: 145, Mismatches: 28, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
38 21 0.14
39 5 0.03
40 3 0.02
41 6 0.04
43 40 0.28
44 35 0.24
46 3 0.02
47 5 0.03
48 27 0.19
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (44 bp):
TGTATTGGAATCATTATTCATTTGCATTTGCAAAATCTTAGTAT
Found at i:18290314 original size:41 final size:41
Alignment explanation
Indices: 18290269--18290390 Score: 109
Period size: 41 Copynumber: 3.1 Consensus size: 41
18290259 AATATAATAA
18290269 TTTTAAATTTTCATATTTTAATTGTAGTTGTTAATAGTTAT
1 TTTTAAATTTTCATATTTTAATTGTAGTTGTTAATAGTTAT
* * * * *
18290310 TTTT--A-TTTCTAAACATTT--TT-T--TTATAAATA-TATAA
1 TTTTAAATTTTC-ATA-TTTTAATTGTAGTTGTTAATAGT-TAT
18290345 TTTTAAATTTTCATATTTTAATTGTAGTTGTTAATAGTTAT
1 TTTTAAATTTTCATATTTTAATTGTAGTTGTTAATAGTTAT
18290386 TTTTA
1 TTTTA
18290391 TTTCTAAACA
Statistics
Matches: 59, Mismatches: 10, Indels: 24
0.63 0.11 0.26
Matches are distributed among these distances:
34 1 0.02
35 13 0.22
36 3 0.05
37 4 0.07
38 12 0.20
39 4 0.07
40 3 0.05
41 18 0.31
42 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (41 bp):
TTTTAAATTTTCATATTTTAATTGTAGTTGTTAATAGTTAT
Found at i:18290352 original size:76 final size:77
Alignment explanation
Indices: 18290253--18290406 Score: 301
Period size: 76 Copynumber: 2.0 Consensus size: 77
18290243 TGAAAACATA
18290253 TTTATAAATATAATAATTTTAAATTTTCATATTTTAATTGTAGTTGTTAATAGTTATTTTTATTT
1 TTTATAAATATAATAATTTTAAATTTTCATATTTTAATTGTAGTTGTTAATAGTTATTTTTATTT
18290318 CTAAACATTTTT
66 CTAAACATTTTT
18290330 TTTATAAATAT-ATAATTTTAAATTTTCATATTTTAATTGTAGTTGTTAATAGTTATTTTTATTT
1 TTTATAAATATAATAATTTTAAATTTTCATATTTTAATTGTAGTTGTTAATAGTTATTTTTATTT
18290394 CTAAACATTTTT
66 CTAAACATTTTT
18290406 T
1 T
18290407 AATTAACAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 66 0.86
77 11 0.14
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (77 bp):
TTTATAAATATAATAATTTTAAATTTTCATATTTTAATTGTAGTTGTTAATAGTTATTTTTATTT
CTAAACATTTTT
Found at i:18290404 original size:41 final size:41
Alignment explanation
Indices: 18290283--18290404 Score: 114
Period size: 37 Copynumber: 3.1 Consensus size: 41
18290273 AAATTTTCAT
18290283 ATTTTAATTGTAGTTGTTAATAGTTATTTTTATTTCTAAAC
1 ATTTTAATTGTAGTTGTTAATAGTTATTTTTATTTCTAAAC
* *** * * * *
18290324 ATTTT--TTTTA-TAAAT-ATA-TAATTTTAAATTT-T-CAT
1 ATTTTAATTGTAGTTGTTAATAGTTATTTT-TATTTCTAAAC
18290359 ATTTTAATTGTAGTTGTTAATAGTTATTTTTATTTCTAAAC
1 ATTTTAATTGTAGTTGTTAATAGTTATTTTTATTTCTAAAC
18290400 ATTTT
1 ATTTT
18290405 TTAATTAACA
Statistics
Matches: 57, Mismatches: 16, Indels: 16
0.64 0.18 0.18
Matches are distributed among these distances:
35 6 0.11
36 7 0.12
37 11 0.19
38 4 0.07
39 11 0.19
40 7 0.12
41 11 0.19
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (41 bp):
ATTTTAATTGTAGTTGTTAATAGTTATTTTTATTTCTAAAC
Found at i:18307023 original size:46 final size:45
Alignment explanation
Indices: 18306953--18307091 Score: 208
Period size: 46 Copynumber: 3.0 Consensus size: 45
18306943 ACAATGCTAT
*
18306953 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTT-ACTGAAATACCATACCTACTTCTCAC
* *
18306999 AACTCAGTATGATTTCCGTTACTGAAATACCATACCTACTTCTCAC
1 AACTCAGTATGGTTTTC-TTACTGAAATACCATACCTACTTCTCAC
18307045 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTC-CAC
1 AACTCAGTATGGTTTTC-TTACTGAAATACCATACCTAC-TTCTCAC
18307091 A
1 A
18307092 CTTTGCCATG
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
46 80 0.94
47 5 0.06
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.35
Consensus pattern (45 bp):
AACTCAGTATGGTTTTCTTACTGAAATACCATACCTACTTCTCAC
Found at i:18313776 original size:34 final size:36
Alignment explanation
Indices: 18313723--18313789 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
18313713 TAACAGAATT
18313723 GATACATAACAACCATACC-ATTTTGGCCATTTAAA
1 GATACATAACAACCATACCAATTTTGGCCATTTAAA
*
18313758 GATACATTAAC-A-CATACCAATTTTGGTCATTT
1 GATACA-TAACAACCATACCAATTTTGGCCATTT
18313790 CAAAACACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 6 0.21
35 19 0.66
36 4 0.14
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (36 bp):
GATACATAACAACCATACCAATTTTGGCCATTTAAA
Found at i:18315026 original size:25 final size:26
Alignment explanation
Indices: 18314992--18315062 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
18314982 CCTATACATA
18314992 TATGCTCACACGAGCTGTG-AATAAG
1 TATGCTCACACGAGCTGTGAAATAAG
* *
18315017 TATGCTCACACGAGCTATGAAAATAGG
1 TATGCTCACACGAGCTGTG-AAATAAG
**
18315044 CCTGCTCACACGAGCTGTG
1 TATGCTCACACGAGCTGTG
18315063 GGTCGAAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 18 0.46
27 21 0.54
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.23
Consensus pattern (26 bp):
TATGCTCACACGAGCTGTGAAATAAG
Found at i:18330437 original size:49 final size:50
Alignment explanation
Indices: 18330347--18330444 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 50
18330337 ACCACACAAC
* * *
18330347 CATGCGGGGCCACATGGGCATGTGGGATTACATGGCAAAATTAGGTAGGT
1 CATGCGGGGCCACACGGGCATGTGCGATTACAGGGCAAAATTAGGTAGGT
* *
18330397 CATGTGGGG-CACACGGGCCTGTGCGATTACACGGGC-AAATTAGGTAGG
1 CATGCGGGGCCACACGGGCATGTGCGATTACA-GGGCAAAATTAGGTAGG
18330445 CCGTACAGGC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 31 0.74
50 11 0.26
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.20
Consensus pattern (50 bp):
CATGCGGGGCCACACGGGCATGTGCGATTACAGGGCAAAATTAGGTAGGT
Found at i:18330722 original size:17 final size:18
Alignment explanation
Indices: 18330700--18330733 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18330690 CGTATTTTGT
*
18330700 TATCTGTTTTGA-TATGA
1 TATCTGATTTGACTATGA
18330717 TATCTGATTTGACTATG
1 TATCTGATTTGACTATG
18330734 TAACAGCCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.50
Consensus pattern (18 bp):
TATCTGATTTGACTATGA
Found at i:18332012 original size:27 final size:27
Alignment explanation
Indices: 18331981--18332051 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
18331971 TTGGTGGTTT
18331981 CTAAGTGCTGATTCCCCCAAGGGGTGG
1 CTAAGTGCTGATTCCCCCAAGGGGTGG
18332008 CTAAGTGCTGATTCCCCCAAGGGGTGG
1 CTAAGTGCTGATTCCCCCAAGGGGTGG
*
18332035 CTAACTGCTGATTCCCC
1 CTAAGTGCTGATTCCCC
18332052 GAATCATTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (27 bp):
CTAAGTGCTGATTCCCCCAAGGGGTGG
Found at i:18335166 original size:26 final size:29
Alignment explanation
Indices: 18335073--18335199 Score: 84
Period size: 26 Copynumber: 4.3 Consensus size: 29
18335063 TGTAAACATT
*
18335073 ATATATAT-T-AGTGGGTGTTATATATATA
1 ATATATATGTGAGTGGTTG-TATATATATA
** * * *
18335101 ATATATAAATGGGGGAGTTGGTAATATACATAA
1 ATATATATGTGAGTG-GTT-GT-ATATATAT-A
*
18335134 ATATATATGTGCGT-G-TGT-TATATATA
1 ATATATATGTGAGTGGTTGTATATATATA
*
18335160 ATATATATATGAGTGGGTTGTATATATATA
1 ATATATATGTGAGT-GGTTGTATATATATA
18335190 CATATATATG
1 -ATATATATG
18335200 CGTGGGAGAT
Statistics
Matches: 75, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
26 13 0.17
27 6 0.08
28 8 0.11
29 6 0.08
30 11 0.15
31 12 0.16
32 8 0.11
33 11 0.15
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (29 bp):
ATATATATGTGAGTGGTTGTATATATATA
Found at i:18335270 original size:39 final size:38
Alignment explanation
Indices: 18335215--18335297 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 38
18335205 GAGATTATTC
*
18335215 ATATAT-TATACATATGCATGGCTTTATTTTAATATAAT
1 ATATATATATACATATGCATGGCTTTATTTT-ATACAAT
* * *
18335253 ATATATATATATATATGCATGGTTTTATTTTATACGAT
1 ATATATATATACATATGCATGGCTTTATTTTATACAAT
18335291 ATATATA
1 ATATATA
18335298 ATTATGCATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 18 0.45
39 22 0.55
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.48
Consensus pattern (38 bp):
ATATATATATACATATGCATGGCTTTATTTTATACAAT
Found at i:18335565 original size:17 final size:17
Alignment explanation
Indices: 18335543--18335575 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18335533 ATTTTTGTAT
18335543 TGTGTTATATT-GTGAAC
1 TGTGTTA-ATTGGTGAAC
18335560 TGTGTTAATTGGTGAA
1 TGTGTTAATTGGTGAA
18335576 TTATATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.45
Consensus pattern (17 bp):
TGTGTTAATTGGTGAAC
Found at i:18335801 original size:7 final size:7
Alignment explanation
Indices: 18335789--18335827 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
18335779 ATCATGCTCT
18335789 ATTGTGA
1 ATTGTGA
18335796 ATTGTGA
1 ATTGTGA
**
18335803 AAGGTGA
1 ATTGTGA
18335810 ATTGTGA
1 ATTGTGA
*
18335817 ATTGCGA
1 ATTGTGA
18335824 ATTG
1 ATTG
18335828 CGAACTGTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.36
Consensus pattern (7 bp):
ATTGTGA
Found at i:18345103 original size:26 final size:29
Alignment explanation
Indices: 18345028--18345136 Score: 80
Period size: 26 Copynumber: 3.7 Consensus size: 29
18345018 NNNTGGGTGT
** * *
18345028 TATATATATAATATATAAATGGGGGAGTTGG
1 TATATATATAATATATATGTGAGTG-GTT-G
* *
18345059 TAATATACATAAATATATATGTGCGT-G-TG
1 T-ATATATAT-AATATATATGTGAGTGGTTG
*
18345088 T-TATATATAATATATATATGAGTGGGTTG
1 TATATATATAATATATATGTGAGT-GGTTG
18345117 TATATATATACATATATATG
1 TATATATATA-ATATATATG
18345137 CGTGGGAGAT
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
26 13 0.21
27 6 0.10
28 1 0.02
29 5 0.08
30 9 0.15
31 10 0.16
32 7 0.11
33 11 0.18
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.40
Consensus pattern (29 bp):
TATATATATAATATATATGTGAGTGGTTG
Found at i:18345207 original size:39 final size:38
Alignment explanation
Indices: 18345152--18345234 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 38
18345142 GAGATTATTC
*
18345152 ATATAT-TATACATATGCATGGCTTTATTTTAATATAAT
1 ATATATATATACATATGCATGGCTTTATTTT-ATACAAT
* * *
18345190 ATATATATATATATATGCATGGTTTTATTTTATACGAT
1 ATATATATATACATATGCATGGCTTTATTTTATACAAT
18345228 ATATATA
1 ATATATA
18345235 ATTATGCGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 18 0.45
39 22 0.55
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.48
Consensus pattern (38 bp):
ATATATATATACATATGCATGGCTTTATTTTATACAAT
Found at i:18345591 original size:17 final size:17
Alignment explanation
Indices: 18345569--18345601 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18345559 ATTTTTGTAT
18345569 TGTGTTATATT-GTGAAC
1 TGTGTTA-ATTGGTGAAC
18345586 TGTGTTAATTGGTGAA
1 TGTGTTAATTGGTGAA
18345602 TTATATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.45
Consensus pattern (17 bp):
TGTGTTAATTGGTGAAC
Found at i:18345827 original size:7 final size:7
Alignment explanation
Indices: 18345815--18345853 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
18345805 ATCATGCTCT
18345815 ATTGTGA
1 ATTGTGA
18345822 ATTGTGA
1 ATTGTGA
**
18345829 AAGGTGA
1 ATTGTGA
18345836 ATTGTGA
1 ATTGTGA
*
18345843 ATTGCGA
1 ATTGTGA
18345850 ATTG
1 ATTG
18345854 CGAACTGTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.36
Consensus pattern (7 bp):
ATTGTGA
Found at i:18363644 original size:28 final size:26
Alignment explanation
Indices: 18363599--18363694 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 26
18363589 TGTAGAAATT
18363599 GAAAA-AAAAAGAATTGAGAGAAAAA
1 GAAAATAAAAAGAATTGAGAGAAAAA
*
18363624 GAGAAATAAAAAGAATGTGAGCGAGAAAA
1 GA-AAATAAAAAGAAT-TGAGAGA-AAAA
** *
18363653 GAAAATTGAAAGAGTTTGAGAAAGAAAAA
1 GAAAATAAAAAGA-ATTGAG--AGAAAAA
18363682 GAAAA-AAAAAGAA
1 GAAAATAAAAAGAA
18363695 AATGGAAAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
25 2 0.04
26 3 0.05
27 9 0.16
28 24 0.43
29 16 0.29
30 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.23, T:0.10
Consensus pattern (26 bp):
GAAAATAAAAAGAATTGAGAGAAAAA
Found at i:18367770 original size:3 final size:3
Alignment explanation
Indices: 18367762--18367796 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
18367752 AAATGTTTGA
*
18367762 AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
18367797 ATGGAGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:18369658 original size:24 final size:25
Alignment explanation
Indices: 18369631--18369683 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
18369621 GCTTTTAACG
18369631 TTTACACGTTTT-ATCATTTT-AGCC
1 TTTACACGTTTTAATCATTTTGA-CC
**
18369655 TTTA-ATTTTTTAATCATTTTGACC
1 TTTACACGTTTTAATCATTTTGACC
18369679 TTTAC
1 TTTAC
18369684 CTTTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 5 0.21
24 18 0.75
25 1 0.04
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.55
Consensus pattern (25 bp):
TTTACACGTTTTAATCATTTTGACC
Found at i:18369883 original size:14 final size:15
Alignment explanation
Indices: 18369864--18369893 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
18369854 ATTAAAAGAC
18369864 ATAATATTT-TTATA
1 ATAATATTTATTATA
18369878 ATAATATTTATTATA
1 ATAATATTTATTATA
18369893 A
1 A
18369894 AAATGATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATAATATTTATTATA
Found at i:18371661 original size:16 final size:17
Alignment explanation
Indices: 18371640--18371671 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18371630 TTTTAAATTT
18371640 TAATTA-AAAATAATAA
1 TAATTACAAAATAATAA
18371656 TAATTACAAAATAATA
1 TAATTACAAAATAATA
18371672 TGTATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATTACAAAATAATAA
Found at i:18371930 original size:20 final size:19
Alignment explanation
Indices: 18371905--18371989 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 19
18371895 AATAAGTTTC
18371905 ACTTAAATTATTTGAATTTT
1 ACTTAAATTATTT-AATTTT
* * *
18371925 ACTTAAATTGTTCAATATAGT
1 ACTTAAATTATTTAAT-T-TT
** *
18371946 AGATAGATTATTTAA-TTT
1 ACTTAAATTATTTAATTTT
18371964 ACTTAAATTATTTAAGTTTT
1 ACTTAAATTATTTAA-TTTT
18371984 ACTTAA
1 ACTTAA
18371990 TAGATAAAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
18 13 0.27
19 4 0.08
20 21 0.43
21 11 0.22
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49
Consensus pattern (19 bp):
ACTTAAATTATTTAATTTT
Found at i:18376341 original size:127 final size:127
Alignment explanation
Indices: 18376131--18377047 Score: 1816
Period size: 127 Copynumber: 7.2 Consensus size: 127
18376121 TGTGTTTTTG
*
18376131 TGTAAGACCATGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
*
18376196 TGGCATCGTATTTGATTTGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATGTGATTACA
66 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
18376258 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
18376323 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
66 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
18376385 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
18376450 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
66 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
18376512 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
18376577 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
66 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
18376639 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
18376704 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
66 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
18376766 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
18376831 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
66 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
18376893 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
18376958 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
66 TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
18377020 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
18377048 TGTACGACTC
Statistics
Matches: 788, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 788 1.00
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (127 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
TGGCATCGTATTTGATTTGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTACA
Found at i:18377237 original size:16 final size:17
Alignment explanation
Indices: 18377208--18377239 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
18377198 TGAATTGATG
18377208 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
18377225 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
18377240 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:18379186 original size:15 final size:15
Alignment explanation
Indices: 18379143--18379192 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
18379133 ATTTAAAATG
18379143 AAAATTTAATTTTA-
1 AAAATTTAATTTTAT
18379157 AATATATTTAA-TTTAT
1 AA-A-ATTTAATTTTAT
18379173 AAAATTTAATTTTAT
1 AAAATTTAATTTTAT
18379188 AAAAT
1 AAAAT
18379193 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.25
15 16 0.50
16 8 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAATTTAATTTTAT
Found at i:18379412 original size:2 final size:2
Alignment explanation
Indices: 18379405--18379435 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
18379395 NNNNNNTGTA
18379405 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18379436 GTTAGGTCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:18380043 original size:2 final size:2
Alignment explanation
Indices: 18380032--18380068 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
18380022 ATGTGAAAAC
18380032 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
18380069 GGGCAGAGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18382364 original size:12 final size:14
Alignment explanation
Indices: 18382331--18382368 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
18382321 TTTAAATGAT
*
18382331 ATTTTTATTAAATA
1 ATTTTTATTTAATA
18382345 ATTTTTATTTAAT-
1 ATTTTTATTTAATA
18382358 A-TTTTATTTAA
1 ATTTTTATTTAA
18382369 AATATTAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 1 0.04
14 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTTATTTAATA
Found at i:18382391 original size:18 final size:20
Alignment explanation
Indices: 18382357--18382393 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
18382347 TTTTATTTAA
18382357 TATTTTATTTAAAATATTAG
1 TATTTTATTTAAAATATTAG
18382377 TATTTTA-TT-AAATATTA
1 TATTTTATTTAAAATATTA
18382394 TTATAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TATTTTATTTAAAATATTAG
Found at i:18385788 original size:91 final size:91
Alignment explanation
Indices: 18385610--18385815 Score: 254
Period size: 91 Copynumber: 2.3 Consensus size: 91
18385600 GATTAATCAT
* * *
18385610 CTGCAAACACTGGTTGTTTATCCACAAACTTACTGGCAACTTTTATCTACAAACAGGTTGTGCAT
1 CTGCAAAAACTGGTGGTTTATCCACAAACTTACTGGCAACTTTTATCTACAAACACGTTGTGCAT
* *
18385675 TCACAACCCACTAGCAGTGTATTAAC
66 TCACAACCCAATAGCAGCGTATTAAC
* * * * *
18385701 TTGTAAAAATTGGTGGTTCATCCAGAAACTTACTGGCAA-TTATTATCTACAAACACGTTGTGCA
1 CTGCAAAAACTGGTGGTTTATCCACAAACTTACTGGCAACTT-TTATCTACAAACACGTTGTGCA
** *
18385765 TTCAGTACCTAAT-GTCAGCGTATTAAC
65 TTCACAACCCAATAG-CAGCGTATTAAC
*
18385792 CTGCAAACACTGGTGGTTTATCCA
1 CTGCAAAAACTGGTGGTTTATCCA
18385816 AAAATTGGAG
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
90 3 0.03
91 92 0.97
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (91 bp):
CTGCAAAAACTGGTGGTTTATCCACAAACTTACTGGCAACTTTTATCTACAAACACGTTGTGCAT
TCACAACCCAATAGCAGCGTATTAAC
Found at i:18388708 original size:30 final size:30
Alignment explanation
Indices: 18388672--18388744 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
18388662 AGATTCGATT
*
18388672 TCTTGATTTTCTTGAAAATAAGAATGTGAA
1 TCTTGATTTTCTTGAAAATAAGAAAGTGAA
18388702 TCTTGATTTTCTTGAAAATAAGAAAGTGAA
1 TCTTGATTTTCTTGAAAATAAGAAAGTGAA
18388732 TCTTGATTTTCTT
1 TCTTGATTTTCTT
18388745 TTTCCTTTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (30 bp):
TCTTGATTTTCTTGAAAATAAGAAAGTGAA
Found at i:18402317 original size:17 final size:18
Alignment explanation
Indices: 18402295--18402337 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
18402285 TAATGAACGT
*
18402295 CAAATAATCAATA-AATA
1 CAAATAAGCAATACAATA
18402312 CAAATAAGCAATACAATA
1 CAAATAAGCAATACAATA
*
18402330 CACATAAG
1 CAAATAAG
18402338 AGCAATAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.60, C:0.16, G:0.05, T:0.19
Consensus pattern (18 bp):
CAAATAAGCAATACAATA
Found at i:18403060 original size:23 final size:23
Alignment explanation
Indices: 18402980--18403095 Score: 96
Period size: 23 Copynumber: 5.0 Consensus size: 23
18402970 TAACAAATAC
* * *
18402980 ATGATAAATGT-AAGTAATGTTA
1 ATGATAAATTTAAAATAATATTA
*
18403002 ATGATAAATTTAAAATAATAATA
1 ATGATAAATTTAAAATAATATTA
*
18403025 CATTG-TAAA-TTAAAATAATATTG
1 -A-TGATAAATTTAAAATAATATTA
18403048 ATGATAAATTTAAAAGTAATATTA
1 ATGATAAATTTAAAA-TAATATTA
* *
18403072 A-GCTTAAATATAAAAATAATATTA
1 ATG-ATAAAT-TTAAAATAATATTA
18403096 GATTTAAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
21 2 0.03
22 15 0.19
23 27 0.35
24 26 0.34
25 7 0.09
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATTA
Found at i:18403080 original size:46 final size:48
Alignment explanation
Indices: 18403002--18403094 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 48
18402992 AGTAATGTTA
*
18403002 ATGATAAATTTAAAATAATAATACATTGTAAAT-T-AAAATAATATTG
1 ATGATAAATTTAAAATAATAATACACTGTAAATATAAAAATAATATTG
*
18403048 ATGATAAATTTAAAAGTAATATTA-AGCT-TAAATATAAAAATAATATT
1 ATGATAAATTTAAAA-TAATAATACA-CTGTAAATATAAAAATAATATT
18403095 AGATTTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
46 21 0.51
47 9 0.22
48 11 0.27
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (48 bp):
ATGATAAATTTAAAATAATAATACACTGTAAATATAAAAATAATATTG
Found at i:18403102 original size:24 final size:23
Alignment explanation
Indices: 18403006--18403109 Score: 79
Period size: 24 Copynumber: 4.4 Consensus size: 23
18402996 ATGTTAATGA
* * *
18403006 TAAATTTAAAATAATAATACATT
1 TAAATTAAAAATAATATTAGATT
*
18403029 GTAAATT-AAAATAATATT-GATGA
1 -TAAATTAAAAATAATATTAGAT-T
* *
18403052 TAAATTTAAAAGTAATATTA-AGCT
1 TAAA-TTAAAAATAATATTAGA-TT
18403076 TAAATATAAAAATAATATTAGATT
1 TAAAT-TAAAAATAATATTAGATT
18403100 TAAAATTAAA
1 T-AAATTAAA
18403110 TATATAAATT
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
22 6 0.09
23 13 0.20
24 40 0.62
25 5 0.08
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (23 bp):
TAAATTAAAAATAATATTAGATT
Found at i:18404182 original size:17 final size:17
Alignment explanation
Indices: 18404160--18404194 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18404150 GGTTACTGTT
18404160 TTAGGCTAGGCTTTGTA
1 TTAGGCTAGGCTTTGTA
* *
18404177 TTAGGCTTGGGTTTGTA
1 TTAGGCTAGGCTTTGTA
18404194 T
1 T
18404195 CGGGATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.09, G:0.31, T:0.46
Consensus pattern (17 bp):
TTAGGCTAGGCTTTGTA
Found at i:18404230 original size:17 final size:19
Alignment explanation
Indices: 18404197--18404235 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
18404187 GTTTGTATCG
*
18404197 GGATTATTTATTTGTAATT
1 GGATTATTTATTTGTAAAT
18404216 GGATT-TTTA-TTGTAAAT
1 GGATTATTTATTTGTAAAT
18404233 GGA
1 GGA
18404236 CATTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 4 0.21
19 5 0.26
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (19 bp):
GGATTATTTATTTGTAAAT
Found at i:18412151 original size:50 final size:50
Alignment explanation
Indices: 18412076--18412177 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
18412066 TTCATTAGTT
*
18412076 CTCCTAATTTTTGTCGGAGGCATTTCCGATAAGATTTCAATCTAGAGAGA
1 CTCCTAATTTTTGTCGGAGGCATTTCCAATAAGATTTCAATCTAGAGAGA
18412126 CTCCTAATTTTTGTCGGAGGCATTTCCAATAAGATTTCAATCTAGAGAGA
1 CTCCTAATTTTTGTCGGAGGCATTTCCAATAAGATTTCAATCTAGAGAGA
18412176 CT
1 CT
18412178 AACTTAATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (50 bp):
CTCCTAATTTTTGTCGGAGGCATTTCCAATAAGATTTCAATCTAGAGAGA
Found at i:18416925 original size:24 final size:23
Alignment explanation
Indices: 18416864--18416938 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
18416854 GTGCTGACCC
*
18416864 ACAGCTCGTGAGAGCATACCGA-TT
1 ACAGCTCGTGTGAGCATA-C-ATTT
* * *
18416888 ATAGCCCGTATGAGCATACTATTT
1 ACAGCTCGTGTGAGCATAC-ATTT
*
18416912 ACAGCTCGTGTGAGCATACATGT
1 ACAGCTCGTGTGAGCATACATTT
18416935 ACAG
1 ACAG
18416939 GATTTGACGA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 9 0.22
24 32 0.78
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (23 bp):
ACAGCTCGTGTGAGCATACATTT
Found at i:18418517 original size:23 final size:25
Alignment explanation
Indices: 18418473--18418519 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
18418463 TATAAGGGGC
*
18418473 AATATGTATTATTTGATTTGATTTT
1 AATATGTATTATTTGATATGATTTT
18418498 AATATGT-TTA-TTGATATGATTT
1 AATATGTATTATTTGATATGATTT
18418520 AAAAAGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 3 0.14
25 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (25 bp):
AATATGTATTATTTGATATGATTTT
Found at i:18418528 original size:22 final size:23
Alignment explanation
Indices: 18418485--18418528 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
18418475 TATGTATTAT
* * *
18418485 TTGATTTGATTTTAATATGTTTA
1 TTGATATGATTTTAAAAAGTTTA
18418508 TTGATATGA-TTTAAAAAGTTT
1 TTGATATGATTTTAAAAAGTTT
18418529 GAAATTTAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (23 bp):
TTGATATGATTTTAAAAAGTTTA
Found at i:18422738 original size:166 final size:167
Alignment explanation
Indices: 18422546--18422879 Score: 661
Period size: 166 Copynumber: 2.0 Consensus size: 167
18422536 CTTACATGGT
18422546 AATTAGACCATTTATAATGTTAGTGGACAAAGATGGGCATGAATTAAGTGTTTTATTTAGTTAAT
1 AATTAGACCATTTATAATGTTAGTGGACAAAGATGGGCATGAATTAAGTGTTTTATTTAGTTAAT
18422611 TAACAAGGTTATTAAACTAATTTAAAAATTAAGTAAAGTAAAATAACATAAAATTAAGTTATCAT
66 TAACAAGGTTATTAAACTAATTTAAAAATTAAGTAAAGTAAAATAACATAAAATTAAGTTATCAT
18422676 CTTCTTTAGTTGAAGTTTCCATGGGAATTATGAGAAG
131 CTTCTTTAGTTGAAGTTTCCATGGGAATTATGAGAAG
18422713 AATTAGACCA-TTATAATGTTAGTGGACAAAGATGGGCATGAATTAAGTGTTTTATTTAGTTAAT
1 AATTAGACCATTTATAATGTTAGTGGACAAAGATGGGCATGAATTAAGTGTTTTATTTAGTTAAT
18422777 TAACAAGGTTATTAAACTAATTTAAAAATTAAGTAAAGTAAAATAACATAAAATTAAGTTATCAT
66 TAACAAGGTTATTAAACTAATTTAAAAATTAAGTAAAGTAAAATAACATAAAATTAAGTTATCAT
18422842 CTTCTTTAGTTGAAGTTTCCATGGGAATTATGAGAAG
131 CTTCTTTAGTTGAAGTTTCCATGGGAATTATGAGAAG
18422879 A
1 A
18422880 GAAAGCCATA
Statistics
Matches: 167, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
166 157 0.94
167 10 0.06
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (167 bp):
AATTAGACCATTTATAATGTTAGTGGACAAAGATGGGCATGAATTAAGTGTTTTATTTAGTTAAT
TAACAAGGTTATTAAACTAATTTAAAAATTAAGTAAAGTAAAATAACATAAAATTAAGTTATCAT
CTTCTTTAGTTGAAGTTTCCATGGGAATTATGAGAAG
Found at i:18425499 original size:26 final size:27
Alignment explanation
Indices: 18425442--18425502 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
18425432 TTTTAGCAAT
** *
18425442 GGTAAAATCGTCAAATATTTTATCGAG
1 GGTAAAATCAACAAATAATTTATCGAG
* *
18425469 AGTAAAATCAACAAA-AATTTATCGGG
1 GGTAAAATCAACAAATAATTTATCGAG
18425495 GGTAAAAT
1 GGTAAAAT
18425503 TTGGATAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (27 bp):
GGTAAAATCAACAAATAATTTATCGAG
Found at i:18430048 original size:40 final size:40
Alignment explanation
Indices: 18429993--18430068 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
18429983 AAAAGATAAG
*
18429993 AAAGATTAGCCTAGAGACAAGCCATGAAAATGGACCTTAA
1 AAAGATTAGCCTAGAGACAAGCCACGAAAATGGACCTTAA
**
18430033 AAAGATTAGCCTAGAGACAAGCGGCGAAAATGGACC
1 AAAGATTAGCCTAGAGACAAGCCACGAAAATGGACC
18430069 CTGAAAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (40 bp):
AAAGATTAGCCTAGAGACAAGCCACGAAAATGGACCTTAA
Found at i:18436812 original size:11 final size:11
Alignment explanation
Indices: 18436785--18436817 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
18436775 ACGATATTTA
*
18436785 ATTTTAGTTTT
1 ATTTTATTTTT
18436796 -TTTTATTTTT
1 ATTTTATTTTT
18436806 ATTTTATTTTT
1 ATTTTATTTTT
18436817 A
1 A
18436818 AGTTGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:18440629 original size:61 final size:61
Alignment explanation
Indices: 18440497--18440613 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
18440487 AAAAACAAAC
* * *
18440497 TGCCACCAAAACTAAAAGATCTAGGGAGTTTCACTGTACCTTGTTCGATTGGAAAGAAAAT
1 TGCCACCAAAACTAAAAGATCCAGGGAGTTTCACTATACCATGTTCGATTGGAAAGAAAAT
* *
18440558 TGCCACCAAAATTAGAAGATCCAGGGAGTTTCACTATACCATGTTCGATTGGAAAG
1 TGCCACCAAAACTAAAAGATCCAGGGAGTTTCACTATACCATGTTCGATTGGAAAG
18440614 CATTATGTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (61 bp):
TGCCACCAAAACTAAAAGATCCAGGGAGTTTCACTATACCATGTTCGATTGGAAAGAAAAT
Found at i:18449740 original size:323 final size:323
Alignment explanation
Indices: 18449152--18449788 Score: 983
Period size: 323 Copynumber: 2.0 Consensus size: 323
18449142 CTAGCTCTCG
*
18449152 TACCTTCGTTTTTGAAACTGTGAAAGATTTTGAATTTTTCCATTGATGAATCAATGTGATTTTAG
1 TACCTTCGTTTTTGAAACCGTGAAAGATTTTGAATTTTTCCATTGATGAATCAATGTGATTTTAG
* * *
18449217 ATGTTAAATGATGAATTTGAAATATTAGTTGATATGTAAAAGTATTTTGTTAAGTGATTTTGTTG
66 ATGTTAAATGATGAATTTGAAATATTAGTGGATATGTAAAAGTATTTTATTAAGTGATTTTGATG
*
18449282 AATTTTCTGATTAGGGACTAAATTGTTGAAATAGTAAAAGTACAAGGTTTTGATATGAAATTGTT
131 AATTTTCTGATTAGGGACTAAATTGTTGAAATAGTAAAAGTACAAGGTTTCGATATGAAATTGTT
* * *
18449347 CAAAAAACTGGCTGAAATGGAGGCTATGAATATTTGGCTAGTGTGAAATTTCAATAAAAATGGTT
196 CAAAAAACTGGCTGAAATGGAGGCTATGAATATTTGGCTAGTGTAAAATTTAAATAAAAATGATT
* *
18449412 AATTTGCA-TGTTTTACCCTTAGGGCCTAAATTGAATAAAAGTAAAACTTTAGGGGCAATTTTA
261 AATTTGCAGT-TTTTACCCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGCAATTTTA
* * * *
18449475 TACCTTCGTTTTTGAAACCGTTAAAGATTTTGAATTTTTCCATTGATGAATTACTGTGCTTTTAG
1 TACCTTCGTTTTTGAAACCGTGAAAGATTTTGAATTTTTCCATTGATGAATCAATGTGATTTTAG
* * * *
18449540 ATGTTTAATGATGAATTTGAAATGTTGGTGGATATTTAAAAGTATTTTATTAAGTGATTTTGATG
66 ATGTTAAATGATGAATTTGAAATATTAGTGGATATGTAAAAGTATTTTATTAAGTGATTTTGATG
* *
18449605 AATTTTTTTATTAGGGACTAAATTGTTGAAATAGTAAAAGTACAAGGTTTCGATATGAAATTGTT
131 AATTTTCTGATTAGGGACTAAATTGTTGAAATAGTAAAAGTACAAGGTTTCGATATGAAATTG-T
* **
18449670 TC-AAAAA-TGAGCTGAAATGGAGGCTGTGAATATTTTTCTAGTGTAAAATTTAAATAAAAATGA
195 TCAAAAAACTG-GCTGAAATGGAGGCTATGAATATTTGGCTAGTGTAAAATTTAAATAAAAATGA
* ** *
18449733 TTAATTTGTAGTTTTTAGGCTCAGGGACTAAATTGAGTAAAAGTAAAACTTTAGGG
259 TTAATTTGCAGTTTTTACCCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGG
18449789 ATAATTTTGT
Statistics
Matches: 284, Mismatches: 27, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
322 2 0.01
323 278 0.98
324 4 0.01
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.39
Consensus pattern (323 bp):
TACCTTCGTTTTTGAAACCGTGAAAGATTTTGAATTTTTCCATTGATGAATCAATGTGATTTTAG
ATGTTAAATGATGAATTTGAAATATTAGTGGATATGTAAAAGTATTTTATTAAGTGATTTTGATG
AATTTTCTGATTAGGGACTAAATTGTTGAAATAGTAAAAGTACAAGGTTTCGATATGAAATTGTT
CAAAAAACTGGCTGAAATGGAGGCTATGAATATTTGGCTAGTGTAAAATTTAAATAAAAATGATT
AATTTGCAGTTTTTACCCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGCAATTTTA
Found at i:18457976 original size:26 final size:26
Alignment explanation
Indices: 18457947--18457996 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
18457937 AAGAAGGCCA
* *
18457947 ATTTC-CAAGCTCGTGTGAGCATATTC
1 ATTTCACAA-CTCATGTGAACATATTC
18457973 ATTTCACAACTCATGTGAACATAT
1 ATTTCACAACTCATGTGAACATAT
18457997 ATGTACATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (26 bp):
ATTTCACAACTCATGTGAACATATTC
Found at i:18460124 original size:20 final size:21
Alignment explanation
Indices: 18460087--18460125 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
18460077 CCGTAGTATG
*
18460087 AAAATTTTCAAATTTTTCCTA
1 AAAATTTTCAAATGTTTCCTA
*
18460108 AAAATTTT-ATATGTTTCC
1 AAAATTTTCAAATGTTTCC
18460126 AATTTAGTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (21 bp):
AAAATTTTCAAATGTTTCCTA
Found at i:18470913 original size:14 final size:14
Alignment explanation
Indices: 18470894--18470925 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
18470884 TTAGGTGATT
18470894 ATATGTGTAATAGG
1 ATATGTGTAATAGG
18470908 ATATGTGTAATAGG
1 ATATGTGTAATAGG
18470922 ATAT
1 ATAT
18470926 ATGCTTAAAA
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:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (14 bp):
ATATGTGTAATAGG
Found at i:18472855 original size:22 final size:22
Alignment explanation
Indices: 18472830--18472871 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
18472820 ATATACACAT
18472830 TTTTTAACTCAAATTCATGCCC
1 TTTTTAACTCAAATTCATGCCC
18472852 TTTTTAACTCAAATTCATGC
1 TTTTTAACTCAAATTCATGC
18472872 AGTTTCGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.43
Consensus pattern (22 bp):
TTTTTAACTCAAATTCATGCCC
Found at i:18498215 original size:20 final size:20
Alignment explanation
Indices: 18498184--18498245 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
18498174 GAAAATAATT
*
18498184 TTAAAATAATTTTAACTTTA
1 TTAAAATCATTTTAACTTTA
* * **
18498204 TTGAAATCATTTTGACTTGG
1 TTAAAATCATTTTAACTTTA
**
18498224 TTAAAATCATTTGCACTTTA
1 TTAAAATCATTTTAACTTTA
18498244 TT
1 TT
18498246 TTAAAATTGT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (20 bp):
TTAAAATCATTTTAACTTTA
Found at i:18505875 original size:24 final size:23
Alignment explanation
Indices: 18505820--18505884 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
18505810 GAAAAGAAAG
*
18505820 AAAAAGTACAAGAAAA-AAGATTGA
1 AAAAAG-A-AAGAAAAGAAAATTGA
18505844 AAAGAAGAAAGAAAAGAAAATTGA
1 AAA-AAGAAAGAAAAGAAAATTGA
18505868 TAAAAAGAAAGGAAAAG
1 -AAAAAGAAA-GAAAAG
18505885 TGAGGAGTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
23 7 0.19
24 17 0.47
25 12 0.33
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (23 bp):
AAAAAGAAAGAAAAGAAAATTGA
Found at i:18519520 original size:17 final size:17
Alignment explanation
Indices: 18519477--18519523 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
18519467 GTTTATTGAT
* *
18519477 TTTTAGTCAATTATTTA
1 TTTTAGTTATTTATTTA
*
18519494 TGTTT-CTTATTTATTTA
1 T-TTTAGTTATTTATTTA
18519511 TTTTAGTTATTTA
1 TTTTAGTTATTTA
18519524 ATTTCTCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 18 0.75
18 3 0.12
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.66
Consensus pattern (17 bp):
TTTTAGTTATTTATTTA
Found at i:18522522 original size:16 final size:16
Alignment explanation
Indices: 18522501--18522531 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
18522491 AAGAAGAAAT
18522501 AAAATGAATGAATGAA
1 AAAATGAATGAATGAA
18522517 AAAATGAATGAATGA
1 AAAATGAATGAATGA
18522532 GTATTGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (16 bp):
AAAATGAATGAATGAA
Found at i:18551299 original size:13 final size:13
Alignment explanation
Indices: 18551281--18551305 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18551271 GAGGAGTTTT
18551281 AGGTGGTGGTTGA
1 AGGTGGTGGTTGA
18551294 AGGTGGTGGTTG
1 AGGTGGTGGTTG
18551306 TTTGTTAACA
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:0.12, C:0.00, G:0.56, T:0.32
Consensus pattern (13 bp):
AGGTGGTGGTTGA
Found at i:18571058 original size:16 final size:17
Alignment explanation
Indices: 18571037--18571070 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18571027 AAATATTATG
18571037 AAATAAA-AGCAAACAA
1 AAATAAACAGCAAACAA
*
18571053 AAATAAACATCAAACAA
1 AAATAAACAGCAAACAA
18571070 A
1 A
18571071 CGCCATCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.74, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
AAATAAACAGCAAACAA
Found at i:18581377 original size:17 final size:17
Alignment explanation
Indices: 18581341--18581379 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
18581331 GTCTCAGCCT
* *
18581341 TGTGAGGCACACGGCTG
1 TGTGAGGCACACGACCG
18581358 TGTGAGGCACACGACCG
1 TGTGAGGCACACGACCG
18581375 TGTGA
1 TGTGA
18581380 CCCCTGCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.23, G:0.38, T:0.18
Consensus pattern (17 bp):
TGTGAGGCACACGACCG
Found at i:18593781 original size:40 final size:40
Alignment explanation
Indices: 18593721--18593822 Score: 141
Period size: 40 Copynumber: 2.5 Consensus size: 40
18593711 AATTATTGAA
* * *
18593721 TGAATGCACACATGTGCCCCTAATTGTACTTCAGTACCTC
1 TGAATGCACATACGTGCCCCTAATTGTACTTCAGTACCCC
* ** *
18593761 TGAATGCACATACGTACCCCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTAATTGTACTTCAGTACCCC
18593801 TGAATGCACATACGTGCCCCTA
1 TGAATGCACATACGTGCCCCTA
18593823 TTTTTACATT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTAATTGTACTTCAGTACCCC
Found at i:18593820 original size:20 final size:20
Alignment explanation
Indices: 18593754--18593821 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
18593744 TTGTACTTCA
*
18593754 GTACCTCTGAATGCACATAC
1 GTACCCCTGAATGCACATAC
** * *
18593774 GTACCCCTGTTTGTAC-TTC
1 GTACCCCTGAATGCACATAC
18593793 GGTACCCCTGAATGCACATAC
1 -GTACCCCTGAATGCACATAC
*
18593814 GTGCCCCT
1 GTACCCCT
18593822 ATTTTTACAT
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.21, C:0.34, G:0.18, T:0.28
Consensus pattern (20 bp):
GTACCCCTGAATGCACATAC
Found at i:18597605 original size:27 final size:27
Alignment explanation
Indices: 18597561--18597669 Score: 139
Period size: 27 Copynumber: 4.1 Consensus size: 27
18597551 TCCGAACGAG
* *
18597561 CTACCCC-TGATTACTGTCTCGGTGGA
1 CTACCCCGTGATTACTGTCCCAGTGGA
**
18597587 CTACCCCGTGATTGTTGTCCCAGTGGA
1 CTACCCCGTGATTACTGTCCCAGTGGA
* *
18597614 CTACCCCGTGATTACTATCCCAGTAGA
1 CTACCCCGTGATTACTGTCCCAGTGGA
* *
18597641 CTACCCCGTGTTTACTGTCCTAGTGGA
1 CTACCCCGTGATTACTGTCCCAGTGGA
18597668 CT
1 CT
18597670 CTATTGGTTG
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
26 7 0.10
27 63 0.90
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.30
Consensus pattern (27 bp):
CTACCCCGTGATTACTGTCCCAGTGGA
Found at i:18600791 original size:50 final size:51
Alignment explanation
Indices: 18600730--18600860 Score: 192
Period size: 50 Copynumber: 2.6 Consensus size: 51
18600720 TATCATTCGA
* * *
18600730 TACACGTAGTAGCCTACACATAGTACTACACACGTGATC-AAACTTTCCAG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCAG
* *
18600780 TTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCAG
* *
18600831 TACGCATAGTAGCCTGCACATAGTACTACA
1 TACACGTAGTAGCCTGCACATAGTACTACA
18600861 TACCGGAAGG
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 36 0.50
51 36 0.50
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCAG
Found at i:18603744 original size:310 final size:310
Alignment explanation
Indices: 18603177--18603785 Score: 1024
Period size: 310 Copynumber: 2.0 Consensus size: 310
18603167 CCTCCAACTC
* *
18603177 AGGGAATTCTGAAATCAATCTCAGCCTACCTCACTAAAATTTAAATATCTCAAAATATACAACTC
1 AGGGAATTCTGAAATCAATCTCACCCTACCTCACTAAAATTCAAATATCTCAAAATATACAACTC
*
18603242 TTTTGCTTGATCTGCTTCTTTTATATAAAAGAAGACTCATTAAGCTTTAATTTCATATCTCATTC
66 TTTTGCTTGATCTGCTTCTTTTATATAAAAGAAGACTCATTAAGCTTTAATTCCATATCTCATTC
** * *
18603307 AACCAATAACTTAATTTCTACAATTTATTGTGATTTTTAAAACTAACATCACTTCCACTGTTCGA
131 AACCAATAACACAATTTCTAAAATTTATTGTGATTTTTAAAACTAACATCACTTCCACTATTCGA
* *
18603372 ATCTGTTCTATTTCAATTTCACTCATTTACATAACATTACAACAATTTATTTTGTAAGCACAGTG
196 ATCTATTCTATTTCAATTTCACTCATTTACATAACATTACAACAATTTATTTTGTAAGCACAGTA
* *
18603437 CGAAACTTCATCACTCCAGTTACTCTTTAGCAAATTTTCCAAGTCAGAAT
261 CAAAACTTCATCACTCCAGTTACTCATTAGCAAATTTTCCAAGTCAGAAT
*
18603487 AGGGGATTCTGAAATCAATC-CGACCCTACCTCACTAAAATTCAAATATCTCAAAATATACAACT
1 AGGGAATTCTGAAATCAATCTC-ACCCTACCTCACTAAAATTCAAATATCTCAAAATATACAACT
* * *
18603551 CTTTTTCTTGATCTGCTTCTTTTATATGAAAGTAGACTCATTAAGCTTTAATTCCATATCTCATT
65 CTTTTGCTTGATCTGCTTCTTTTATATAAAAGAAGACTCATTAAGCTTTAATTCCATATCTCATT
* *
18603616 CAATCAATAACACAATTTCTAAAATTT-TTGGTGATTTTTCAAACTAACATCACTTCCACTATTC
130 CAACCAATAACACAATTTCTAAAATTTATT-GTGATTTTTAAAACTAACATCACTTCCACTATTC
*
18603680 GAATCTATTCTGTTTCAATTTCACTCATTTACATAACATTACAACAATTTATTTTGTAAGCACAG
194 GAATCTATTCTATTTCAATTTCACTCATTTACATAACATTACAACAATTTATTTTGTAAGCACAG
18603745 TACAAAACTTCATCACTCCAGTTACTCATTAGCAAATTTTC
259 TACAAAACTTCATCACTCCAGTTACTCATTAGCAAATTTTC
18603786 ACACTTCAAT
Statistics
Matches: 279, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
309 3 0.01
310 276 0.99
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (310 bp):
AGGGAATTCTGAAATCAATCTCACCCTACCTCACTAAAATTCAAATATCTCAAAATATACAACTC
TTTTGCTTGATCTGCTTCTTTTATATAAAAGAAGACTCATTAAGCTTTAATTCCATATCTCATTC
AACCAATAACACAATTTCTAAAATTTATTGTGATTTTTAAAACTAACATCACTTCCACTATTCGA
ATCTATTCTATTTCAATTTCACTCATTTACATAACATTACAACAATTTATTTTGTAAGCACAGTA
CAAAACTTCATCACTCCAGTTACTCATTAGCAAATTTTCCAAGTCAGAAT
Found at i:18611422 original size:51 final size:51
Alignment explanation
Indices: 18611346--18611537 Score: 253
Period size: 51 Copynumber: 3.8 Consensus size: 51
18611336 TGAAAGTGAA
* * *
18611346 AGTGATGGTCACGTGTCTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
1 AGTGATAGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
* * * *
18611397 AGTGATAGTCACATGTGTAGTACTATGTGCAGGCCACTATGCGTACCGGAT
1 AGTGATAGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
* *
18611448 AGCT--TCGATCACTTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
1 AG-TGATAG-TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
* *
18611499 AGTGATAGTCACATGTGTAGTACTATGTGTACGCTACTA
1 AGTGATAGTCACATGTGTAGTACTATGTGCAGGCTACTA
18611538 TGTGAATCAG
Statistics
Matches: 120, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
50 3 0.03
51 114 0.95
52 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (51 bp):
AGTGATAGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
Found at i:18611538 original size:102 final size:102
Alignment explanation
Indices: 18611354--18611539 Score: 327
Period size: 102 Copynumber: 1.8 Consensus size: 102
18611344 AAAGTGATGG
18611354 TCACGTGTCTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATAGTCACATGTGTAGTA
1 TCACGTGTCTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATAGTCACATGTGTAGTA
*
18611419 CTATGTGCAGGCCACTATGCGTACCGGATAGCTTCGA
66 CTATGTGCACGCCACTATGCGTACCGGATAGCTTCGA
* *
18611456 TCACTTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATAGTCACATGTGTAGTA
1 TCACGTGTCTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATAGTCACATGTGTAGTA
* *
18611521 CTATGTGTACGCTACTATG
66 CTATGTGCACGCCACTATG
18611540 TGAATCAGTA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 79 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (102 bp):
TCACGTGTCTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATAGTCACATGTGTAGTA
CTATGTGCACGCCACTATGCGTACCGGATAGCTTCGA
Found at i:18618919 original size:28 final size:27
Alignment explanation
Indices: 18618862--18618921 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 27
18618852 AAAGTCTTTT
18618862 TTTTTTAAATTTACCGAAATAGGCCGG
1 TTTTTTAAATTTACCGAAATAGGCCGG
* *
18618889 TTTTTTAATTATTTACCGGAATGGGCC-G
1 TTTTTTAA--ATTTACCGAAATAGGCCGG
18618917 TTTTT
1 TTTTT
18618922 CCCGAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.28
28 6 0.21
29 15 0.52
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.45
Consensus pattern (27 bp):
TTTTTTAAATTTACCGAAATAGGCCGG
Found at i:18619216 original size:22 final size:22
Alignment explanation
Indices: 18619191--18619259 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
18619181 ACAAATCCTA
*
18619191 TCTCAATTTCATTCAAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
**
18619213 TCTCAAAGTCCTTCAAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
*
18619235 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
18619257 TCT
1 TCT
18619260 TAAACTCTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.32, C:0.28, G:0.01, T:0.39
Consensus pattern (22 bp):
TCTCAATTTCCTTCAAAAATTC
Found at i:18619294 original size:52 final size:51
Alignment explanation
Indices: 18619212--18619317 Score: 140
Period size: 52 Copynumber: 2.1 Consensus size: 51
18619202 TTCAAAAATT
* * * *
18619212 CTCTCAAAGTCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTTAAA
1 CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTC-TAAA
* * *
18619264 CTCTCGAATTCCTTCCAAAATCCTCACAATTTCCTTCAAAAAATCTCTAAA
1 CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCTAAA
18619315 CTC
1 CTC
18619318 CATATTAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 7 0.15
52 40 0.85
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.34
Consensus pattern (51 bp):
CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCTAAA
Found at i:18619386 original size:29 final size:28
Alignment explanation
Indices: 18619348--18619405 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 28
18619338 ATTCAATTTC
18619348 ATTTTTTTAAGAA-AATTTTAAATATTTTT
1 ATTTTTTTAA-AATAATTTT-AATATTTTT
18619377 ATTTTTTTAAAATAATTTTAATATTTTT
1 ATTTTTTTAAAATAATTTTAATATTTTT
18619405 A
1 A
18619406 ATATTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
ATTTTTTTAAAATAATTTTAATATTTTT
Found at i:18619395 original size:19 final size:20
Alignment explanation
Indices: 18619363--18619406 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
18619353 TTTAAGAAAA
* *
18619363 TTTT-AAAT-ATTTTTATTT
1 TTTTAAAATAATTTTAATAT
18619381 TTTTAAAATAATTTTAATAT
1 TTTTAAAATAATTTTAATAT
18619401 TTTTAA
1 TTTTAA
18619407 TATTTTCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAAATAATTTTAATAT
Found at i:18619412 original size:28 final size:29
Alignment explanation
Indices: 18619352--18619412 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
18619342 AATTTCATTT
* *
18619352 TTTTAAGAAAATTTTAAATATTTTTATTT
1 TTTTAAGAAAATTTTAAATATTTTTAATA
18619381 TTTTAA-AATAATTTT-AATATTTTTAATA
1 TTTTAAGAA-AATTTTAAATATTTTTAATA
18619409 TTTT
1 TTTT
18619413 CAACAATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTAAGAAAATTTTAAATATTTTTAATA
Found at i:18619412 original size:29 final size:29
Alignment explanation
Indices: 18619351--18619412 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
18619341 CAATTTCATT
*
18619351 TTTTTAAGAAAATTTTAAATATTTTTATT
1 TTTTTAAGAAAATTTTAAATATTTTTATA
18619380 TTTTTAA-AATAATTTT-AATATTTTTAATA
1 TTTTTAAGAA-AATTTTAAATATTTTT-ATA
18619409 TTTT
1 TTTT
18619413 CAACAATGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTAAGAAAATTTTAAATATTTTTATA
Found at i:18620229 original size:7 final size:7
Alignment explanation
Indices: 18620217--18620241 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18620207 NNNNNNTTGA
18620217 TATTTAG
1 TATTTAG
18620224 TATTTAG
1 TATTTAG
18620231 TATTTAG
1 TATTTAG
18620238 TATT
1 TATT
18620242 ATGTATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:18621833 original size:30 final size:31
Alignment explanation
Indices: 18621787--18621914 Score: 178
Period size: 29 Copynumber: 4.3 Consensus size: 31
18621777 NNNNNNNNNN
18621787 ATTTAATTAT-AAACCCT-AACCCTAACCTA
1 ATTTAATTATAAAACCCTAAACCCTAACCTA
*
18621816 ATTCAATTATAAAACCCT-AA-CCTAACCTA
1 ATTTAATTATAAAACCCTAAACCCTAACCTA
18621845 ATTTAATTA-AAAACCCTAAACCCTAACCTA
1 ATTTAATTATAAAACCCTAAACCCTAACCTA
* *
18621875 ATTTAATT-TAATTAGCCTAAACCCTAACCTA
1 ATTTAATTATAA-AACCCTAAACCCTAACCTA
18621906 ATTTAATTA
1 ATTTAATTA
18621915 AATTAAACGA
Statistics
Matches: 89, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
28 8 0.09
29 28 0.31
30 28 0.31
31 25 0.28
ACGTcount: A:0.43, C:0.24, G:0.01, T:0.32
Consensus pattern (31 bp):
ATTTAATTATAAAACCCTAAACCCTAACCTA
Found at i:18621897 original size:31 final size:31
Alignment explanation
Indices: 18621798--18621913 Score: 152
Period size: 31 Copynumber: 3.9 Consensus size: 31
18621788 TTTAATTATA
*
18621798 AACCCT-AACCCTAACCTAATTCAATTATAA-
1 AACCCTAAACCCTAACCTAATTTAATT-TAAT
*
18621828 AACCCT-AA-CCTAACCTAATTTAA-TTAAA
1 AACCCTAAACCCTAACCTAATTTAATTTAAT
18621856 AACCCTAAACCCTAACCTAATTTAATTTAAT
1 AACCCTAAACCCTAACCTAATTTAATTTAAT
* *
18621887 TAGCCTAAACCCTAACCTAATTTAATT
1 AACCCTAAACCCTAACCTAATTTAATT
18621914 AAATTAAACG
Statistics
Matches: 78, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
27 3 0.04
28 7 0.09
29 16 0.21
30 23 0.29
31 29 0.37
ACGTcount: A:0.42, C:0.27, G:0.01, T:0.30
Consensus pattern (31 bp):
AACCCTAAACCCTAACCTAATTTAATTTAAT
Found at i:18621919 original size:31 final size:30
Alignment explanation
Indices: 18621787--18621916 Score: 176
Period size: 30 Copynumber: 4.4 Consensus size: 30
18621777 NNNNNNNNNN
*
18621787 ATTTAATTATAAACCCT-AACCCTAACCTA
1 ATTTAATTAAAAACCCTAAACCCTAACCTA
*
18621816 ATTCAATTATAAAACCCT-AA-CCTAACCTA
1 ATTTAATTA-AAAACCCTAAACCCTAACCTA
18621845 ATTTAATTAAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAAACCCTAACCTA
** *
18621875 ATTTAATTTAATTAGCCTAAACCCTAACCTA
1 ATTTAA-TTAAAAACCCTAAACCCTAACCTA
18621906 ATTTAATTAAA
1 ATTTAATTAAA
18621917 TTAAACGACG
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
28 8 0.09
29 27 0.30
30 28 0.31
31 27 0.30
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.32
Consensus pattern (30 bp):
ATTTAATTAAAAACCCTAAACCCTAACCTA
Found at i:18623372 original size:125 final size:125
Alignment explanation
Indices: 18622842--18623357 Score: 901
Period size: 125 Copynumber: 4.1 Consensus size: 125
18622832 CACGAGGGCA
*
18622842 CGATTTTACACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCA
1 CGATTTTACACTATTTGCTCAAAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCA
18622907 AAATCGCGTCCACGAGGGCGCGATTTCAAAATTTATTCTCATATAGCATCCTGGTATCAG
66 AAATCGCGTCCACGAGGGCGCGATTTCAAAATTTATTCTCATATAGCATCCTGGTATCAG
18622967 CGATTTTACACTATTTGCTCAAAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCA
1 CGATTTTACACTATTTGCTCAAAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCA
18623032 AAATCGCGTCCACGAGGGCGCGATTTCAAAATTTATTCTCATATAGCATCCTGGTATCAG
66 AAATCGCGTCCACGAGGGCGCGATTTCAAAATTTATTCTCATATAGCATCCTGGTATCAG
* *
18623092 CGATTTTACACTATTTGCTCAAAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTTGCG
1 CGATTTTACACTATTTGCTCAAAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCA
18623157 AAATCGCGTCCACGAGGGCGCGATTTCAAAATTTATTCTCATATAGCATCCTGGTATCAG
66 AAATCGCGTCCACGAGGGCGCGATTTCAAAATTTATTCTCATATAGCATCCTGGTATCAG
*
18623217 CGATTTTACACTATTTGCTCAAAAACGTCAAAAAAAAATTATTTCTTACATGACCAACTGT-GCT
1 CGATTTTACACTATTTGCTCAAAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGC-
* * * * **
18623281 AAAATGGCGTCCACGAGGGCACGATTTCACAATTTCTTCTC-TGATAGCATCCTGGTAGAAG
65 AAAATCGCGTCCACGAGGGCGCGATTTCAAAATTTATTCTCAT-ATAGCATCCTGGTATCAG
*
18623342 CGATTTTATACTATTT
1 CGATTTTACACTATTT
18623358 TACCAGAAAC
Statistics
Matches: 377, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
124 3 0.01
125 374 0.99
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (125 bp):
CGATTTTACACTATTTGCTCAAAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCA
AAATCGCGTCCACGAGGGCGCGATTTCAAAATTTATTCTCATATAGCATCCTGGTATCAG
Found at i:18623452 original size:52 final size:50
Alignment explanation
Indices: 18623375--18623530 Score: 249
Period size: 52 Copynumber: 3.0 Consensus size: 50
18623365 AACGTCAACT
18623375 CGAAATAATTTTTTTGGGACCCCTAAACCCTAAAAAAGCATGCACCCTAAA
1 CGAAATAATTTTTTTGGGACCCCTAAACCCTAAAAAAGC-TGCACCCTAAA
* *
18623426 CGAAATACTTTTTTTCGGCACCCCTAAACCCTAAAAAAGTCTGCACCCTAAA
1 CGAAATAATTTTTTT-GGGACCCCTAAACCCTAAAAAAG-CTGCACCCTAAA
18623478 CGAAATAATTTTTTTTGGGACCCCTAAACCCTAAAAAAGCTTGCACCCTAAA
1 CGAAATAA-TTTTTTTGGGACCCCTAAACCCTAAAAAAGC-TGCACCCTAAA
18623530 C
1 C
18623531 CCTAAAACCC
Statistics
Matches: 97, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
51 15 0.15
52 74 0.76
53 8 0.08
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.25
Consensus pattern (50 bp):
CGAAATAATTTTTTTGGGACCCCTAAACCCTAAAAAAGCTGCACCCTAAA
Found at i:18623769 original size:28 final size:27
Alignment explanation
Indices: 18623710--18623768 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
18623700 GATTTCGGGG
18623710 AAAACGGCCCATTCCGGTAAATAATTAA
1 AAAACGGCCCATTCCGGTAAAT-ATTAA
* *
18623738 AAAACCGGCCTATTTCGGTAAAT-TTAA
1 AAAA-CGGCCCATTCCGGTAAATATTAA
18623765 AAAA
1 AAAA
18623769 AAAGGGCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.29
28 4 0.14
29 16 0.57
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.24
Consensus pattern (27 bp):
AAAACGGCCCATTCCGGTAAATATTAA
Found at i:18629357 original size:33 final size:33
Alignment explanation
Indices: 18629319--18629388 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
18629309 GGAGGCTCAC
18629319 CTTTAGGA-ATAGGAAAACAAAATTCAGTTTTAA
1 CTTTAGGAGA-AGGAAAACAAAATTCAGTTTTAA
* * *
18629352 CTTTAGGAGAAGGAAAACAAAGTTCGGTTTTAC
1 CTTTAGGAGAAGGAAAACAAAATTCAGTTTTAA
18629385 CTTT
1 CTTT
18629389 TCCATTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (33 bp):
CTTTAGGAGAAGGAAAACAAAATTCAGTTTTAA
Found at i:18630290 original size:12 final size:13
Alignment explanation
Indices: 18630266--18630299 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
18630256 TCGTTTTCTC
18630266 TTCTTTCTTCAA-T
1 TTCTTT-TTCAATT
18630279 TTCTTTTTCAATT
1 TTCTTTTTCAATT
18630292 TTCTTTTT
1 TTCTTTTT
18630300 TTCACATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (13 bp):
TTCTTTTTCAATT
Found at i:18632127 original size:7 final size:6
Alignment explanation
Indices: 18632082--18632146 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
18632072 CTCACTCTCA
* * * * *
18632082 TTTTCT TTTTCA ATTTCT TGTTCT CTTTCT TTTTCT TTTTCA TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
18632130 TTTCTCGTT TTTTCT TT
1 TTT-TC--T TTTTCT TT
18632147 ACAAGATAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
6 38 0.83
7 2 0.04
8 2 0.04
9 4 0.09
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (6 bp):
TTTTCT
Found at i:18635562 original size:24 final size:22
Alignment explanation
Indices: 18635525--18635575 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
18635515 AATTATTTAA
18635525 TTTTAAATAGTTAATTATTATGAT
1 TTTTAAATAGTTAA-TATT-TGAT
*
18635549 TTTTAAATTA-TTAATATTTTAT
1 TTTTAAA-TAGTTAATATTTGAT
18635571 TTTTA
1 TTTTA
18635576 TATACTCAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 8 0.32
23 4 0.16
24 11 0.44
25 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTTAAATAGTTAATATTTGAT
Found at i:18641772 original size:42 final size:42
Alignment explanation
Indices: 18641716--18641807 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
18641706 ATTGATCAAG
18641716 AGTAATATAACTTGATTTTGGACAAAAAATTATAACTATTCA
1 AGTAATATAACTTGATTTTGGACAAAAAATTATAACTATTCA
* **
18641758 AGTATTATAACTTGATTTTTTACAAAAAATTATAACTATTCA
1 AGTAATATAACTTGATTTTGGACAAAAAATTATAACTATTCA
*
18641800 AATAATAT
1 AGTAATAT
18641808 TACCTGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (42 bp):
AGTAATATAACTTGATTTTGGACAAAAAATTATAACTATTCA
Found at i:18645760 original size:24 final size:24
Alignment explanation
Indices: 18645728--18645776 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
18645718 CTGCCTTGGT
*
18645728 TTACCCTTGCTTTTGTAGACTCTC
1 TTACCCTTGCTTTTGCAGACTCTC
18645752 TTACCCTTGCTTTTGCAGACTCTC
1 TTACCCTTGCTTTTGCAGACTCTC
18645776 T
1 T
18645777 CAACATGACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.31, G:0.12, T:0.45
Consensus pattern (24 bp):
TTACCCTTGCTTTTGCAGACTCTC
Found at i:18647284 original size:11 final size:11
Alignment explanation
Indices: 18647254--18647288 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
18647244 ACTTTATTTT
*
18647254 TTTTGTTCGAG
1 TTTTGTTCGTG
18647265 TTATTGTTCGTG
1 TT-TTGTTCGTG
18647277 TTTTGTTCGTG
1 TTTTGTTCGTG
18647288 T
1 T
18647289 GTTGAAGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.06, C:0.09, G:0.26, T:0.60
Consensus pattern (11 bp):
TTTTGTTCGTG
Found at i:18651655 original size:1 final size:1
Alignment explanation
Indices: 18651649--18651674 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
18651639 CTATCACTAC
18651649 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
18651675 TTCATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18652345 original size:19 final size:20
Alignment explanation
Indices: 18652300--18652345 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
18652290 TTTTATTATT
18652300 TTAATTCTTGATTAATTATGA
1 TTAATT-TTGATTAATTATGA
* *
18652321 -TGATTTTGTTTAATT-TGA
1 TTAATTTTGATTAATTATGA
18652339 TTAATTT
1 TTAATTT
18652346 CTATATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 3 0.14
19 14 0.67
20 4 0.19
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (20 bp):
TTAATTTTGATTAATTATGA
Found at i:18658917 original size:40 final size:40
Alignment explanation
Indices: 18658820--18658986 Score: 129
Period size: 40 Copynumber: 4.2 Consensus size: 40
18658810 TTGAACAACT
*
18658820 TTCAGTAGGTATGGCTTGATAGAACATACTTTTCAGTGGA
1 TTCAGTAGGTATGGCTCGATAGAACATACTTTTCAGTGGA
* * * * * * *
18658860 ATCAATATGTATAGCTCGATGGAGCCTACTTTGT-AGTGGA
1 TTCAGTAGGTATGGCTCGATAGAACATACTTT-TCAGTGGA
* ** * * *
18658900 TTCAGTAGGTATGGCTCGAAAGCGCATACGTTTCAATAGA
1 TTCAGTAGGTATGGCTCGATAGAACATACTTTTCAGTGGA
* * *** * *
18658940 TTCAGTAGCTATGGTTCGATATTGCATACATTTCAGTAGA
1 TTCAGTAGGTATGGCTCGATAGAACATACTTTTCAGTGGA
18658980 TTCAGTA
1 TTCAGTA
18658987 AATACCACTC
Statistics
Matches: 99, Mismatches: 26, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
39 1 0.01
40 97 0.98
41 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (40 bp):
TTCAGTAGGTATGGCTCGATAGAACATACTTTTCAGTGGA
Found at i:18660771 original size:20 final size:19
Alignment explanation
Indices: 18660746--18660860 Score: 88
Period size: 20 Copynumber: 5.8 Consensus size: 19
18660736 TTGTACGGGA
18660746 TTTGCACTTTGGTGCCTCTG
1 TTTGCACTTTGGTGCC-CTG
**
18660766 TTTGCACTTCAGTGCCCCTG
1 TTTGCACTTTGGTG-CCCTG
* *
18660786 TATACACTTTGGTGTCCCTG
1 TTTGCACTTTGGTG-CCCTG
* * *
18660806 TTCGCACTATGGTGCCCTTT
1 TTTGCACTTTGGTGCCC-TG
* *
18660826 TTTGTACATTT-GTGCCCCTA
1 TTTGCAC-TTTGGTG-CCCTG
18660846 TTTGCACTTTGGTGC
1 TTTGCACTTTGGTGC
18660861 TCTTGTTATG
Statistics
Matches: 73, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
19 7 0.10
20 59 0.81
21 7 0.10
ACGTcount: A:0.10, C:0.27, G:0.21, T:0.42
Consensus pattern (19 bp):
TTTGCACTTTGGTGCCCTG
Found at i:18668336 original size:24 final size:24
Alignment explanation
Indices: 18668309--18668355 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
18668299 ATTACCAATG
* *
18668309 AAAACCTCCTCTAATAATAGTAAA
1 AAAACCTCCTATAATAACAGTAAA
18668333 AAAACCTCCTATAATAACAGTAA
1 AAAACCTCCTATAATAACAGTAA
18668356 CATGGTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.23
Consensus pattern (24 bp):
AAAACCTCCTATAATAACAGTAAA
Found at i:18676579 original size:13 final size:14
Alignment explanation
Indices: 18676561--18676589 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
18676551 AAAATTGCTT
18676561 AAAAATCAAG-CAA
1 AAAAATCAAGTCAA
18676574 AAAAATCAAGTCAA
1 AAAAATCAAGTCAA
18676588 AA
1 AA
18676590 GCCACTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATCAAGTCAA
Done.