Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold171
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: 2364178
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 278680 characters in sequence are not A, C, G, or T
File 7 of 13
Found at i:1093543 original size:28 final size:28
Alignment explanation
Indices: 1092563--1093547 Score: 729
Period size: 28 Copynumber: 35.1 Consensus size: 28
1092553 TGAAAAGGGT
* *
1092563 TGCCACTGACTTATGTGGGCCTTGAAAAGAGG
1 TGCCACTGAC-T-TGTGGGCTTTG--AAGAGA
* *
1092595 TGCCACTGACCTGTGGGCTTTGGAAGA-T
1 TGCCACTGACTTGTGGGCTTT-GAAGAGA
** ** * *
1092623 TGCCACCAACTTGTGGGCTTAAAAGGGG
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
** * * *
1092651 TGCCACTTTCTTGTTGACTTTGGAAG-GG
1 TGCCACTGACTTGTGGGCTTT-GAAGAGA
** * * *
1092679 TGCCACCAACTTGTGGGC-TTAAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAGA-GA
* *
1092707 TGCCATTGACTTGTGGACTTTGAA-AGGA
1 TGCCACTGACTTGTGGGCTTTGAAGA-GA
* *
1092735 TGCCATTGACCTGTGGGCTTTGAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
1092763 TGCCACTGACTTGTGGGCTTTGAA-AGAA
1 TGCCACTGACTTGTGGGCTTTGAAGAG-A
* * * *
1092791 TGCCACTAACCTGTGGGTTTTAAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
* *
1092819 TGCCACTAACTTGTGGGTTTTGAA-ATGA
1 TGCCACTGACTTGTGGGCTTTGAAGA-GA
* * * *
1092847 TGCCACTAACCTGTGGACTTTAAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
*
1092875 TGCCACTAACTTGTGGGCTTTGAA-AGGA
1 TGCCACTGACTTGTGGGCTTTGAAGA-GA
* * *
1092903 TGCCATTGACATGTGGGCTTTAAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
* *
1092931 TGCCACTAACTTGTAGGCTTTGGAAG-GA
1 TGCCACTGACTTGTGGGCTTT-GAAGAGA
* *
1092959 TGCCACTGACTTGTGGGCTTTCAAGGGA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
* * *
1092987 TGTCATTGACTTGTGGGCTTT-AAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAGA-GA
* * *
1093015 TTCCACTAACCTGTGGGCTTTGAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
* * *
1093043 TGTCACTGACTTATTGGCTTTGAA-AGGA
1 TGCCACTGACTTGTGGGCTTTGAAGA-GA
* * * * *
1093071 TGCCGCCGACCTATGGGCTTTAGAAG-GG
1 TGCCACTGACTTGTGGGCTTT-GAAGAGA
* * * *
1093099 TGCCA-TCGACTTTTGGGC-TTAAAAAGGG
1 TGCCACT-GACTTGTGGGCTTTGAAGA-GA
* * *
1093127 TGCTACTTG-CTTGTGGGCATTGGAAG-GG
1 TGCCAC-TGACTTGTGGGC-TTTGAAGAGA
* * * * *
1093155 TGCCACCGACTTGTGGG-ATTAAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAGA-GA
* *
1093183 TGCTACTGACTTGTGGACTTTGAA-AGGA
1 TGCCACTGACTTGTGGGCTTTGAAGA-GA
* *
1093211 TGCCATTGACCTGTGGGCTTTGAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
* *
1093239 TGCCACTGAATTATGGGCTTTGAA-AGGA
1 TGCCACTGACTTGTGGGCTTTGAAGA-GA
* *
1093267 TGCCACTAACTTATGGGCTTTGAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
*
1093295 TGCCACTAACTTGTGGGCTTTGAA-AGGA
1 TGCCACTGACTTGTGGGCTTTGAAGA-GA
* * *
1093323 TGCCATTGACCTGTGGACTTTGAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
* * *
1093351 TGCTATTGACTTGTGGGCTTT-AAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAGA-GA
* * *
1093379 TGCCACTGACCTATGGACTTTGAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
*
1093407 TGCCACTGACTTGTAGGCTTTGGAAG-GA
1 TGCCACTGACTTGTGGGCTTT-GAAGAGA
* * *
1093435 TGCCATTGACTTGTGGGCTTTCAAGAAA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
*
1093463 TGCCACTGACTTATGGGCTTTGAA-AGGA
1 TGCCACTGACTTGTGGGCTTTGAAGA-GA
* *
1093491 TGCCA-TGACCTGTGGGCTTTGAAGAAA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
*
1093518 TGCCACTGACTTGTGGGCTTTCAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAGAGA
1093546 TG
1 TG
1093548 AACGTTCTAG
Statistics
Matches: 763, Mismatches: 147, Indels: 90
0.76 0.15 0.09
Matches are distributed among these distances:
26 7 0.01
27 49 0.06
28 643 0.84
29 40 0.05
30 13 0.02
31 1 0.00
32 10 0.01
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTGAAGAGA
Found at i:1102258 original size:13 final size:13
Alignment explanation
Indices: 1102240--1102267 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1102230 TTACAAAGAT
1102240 CAATGTATCGATA
1 CAATGTATCGATA
1102253 CAATGTATCGATA
1 CAATGTATCGATA
1102266 CA
1 CA
1102268 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1103265 original size:49 final size:49
Alignment explanation
Indices: 1103055--1103453 Score: 199
Period size: 49 Copynumber: 8.4 Consensus size: 49
1103045 ATAAACGGCT
* * * * * *
1103055 AGCGATATTGGGCTCAAAGATGCGAAGAATGACAATGTGCTGATTCATGGCC
1 AGCGACATTGGACTTAAAGAT--GAA-AATGCCAATATGCTGATTCAAGGCC
* * * * * * **
1103107 AGTGACATTAGATTTAAAGA--AGAATGCCAATGTGCTCAGACAAGGCC
1 AGCGACATTGGACTTAAAGATGAAAATGCCAATATGCTGATTCAAGGCC
* ** * * *
1103154 AGCGACATTGGGCTTAGGGACGTTAAAGATGTCAGTATGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGA--TGAAA-ATGCCAATATGCTGATTCAAGGCC
* * * *
1103206 AACGATATTGGACTTAAAGATGAAAATGCCAATGTGCTGATTCAAGACC
1 AGCGACATTGGACTTAAAGATGAAAATGCCAATATGCTGATTCAAGGCC
* * ** * *
1103255 AGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCCGATTCAAAGCC
1 AGCGACATTGGACTTAAAGATGAAAATGCCAATATGCTGATTCAAGGCC
* * * *
1103303 AACGATATTGGGC-T-----T----ATGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAAATGCCAATATGCTGATTCAAGGCC
* * * *** *
1103342 AACAACATTGGTCTTAAAGATGCCGATGCCAATATGCTGATTTAAGGCC
1 AGCGACATTGGACTTAAAGATGAAAATGCCAATATGCTGATTCAAGGCC
* *
1103391 AGTGACATT-GACTTAAA-A-G----TGCCAATATGCTGAGTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAAATGCCAATATGCTGATTCAAGGCC
*
1103433 AGCGATATTGGACTTAGAAGA
1 AGCGACATTGGACTTA-AAGA
1103454 AGATGCCACC
Statistics
Matches: 263, Mismatches: 65, Indels: 45
0.71 0.17 0.12
Matches are distributed among these distances:
39 30 0.11
40 1 0.00
42 28 0.11
43 6 0.02
44 2 0.01
45 2 0.01
46 1 0.00
47 36 0.14
48 39 0.15
49 65 0.25
50 4 0.02
51 2 0.01
52 47 0.18
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
AGCGACATTGGACTTAAAGATGAAAATGCCAATATGCTGATTCAAGGCC
Found at i:1103313 original size:48 final size:49
Alignment explanation
Indices: 1103189--1103318 Score: 147
Period size: 48 Copynumber: 2.7 Consensus size: 49
1103179 AAGATGTCAG
* *
1103189 TATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAAATGCCAA
1 TATGCTGATTCAAAGCCAACGATATTGGACTTAAAGATCAAAATGCCAA
* * * * **
1103238 TGTGCTGATTC-AAGACCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAA
1 TATGCTGATTCAAAG-CCAACGATATTGGACTTAAAGATCAAAATGCCAA
* *
1103286 TATGCCGATTCAAAGCCAACGATATTGGGCTTA
1 TATGCTGATTCAAAGCCAACGATATTGGACTTA
1103319 TGCCAATGTG
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
48 34 0.52
49 32 0.48
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (49 bp):
TATGCTGATTCAAAGCCAACGATATTGGACTTAAAGATCAAAATGCCAA
Found at i:1103352 original size:39 final size:39
Alignment explanation
Indices: 1103280--1103357 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
1103270 AAAGACAAGG
* *
1103280 TGCCAATATGCCGATTCAAAGCCAACGATATTGGGCTTA
1 TGCCAATATGCCGATTCAAAGCCAACAACATTGGGCTTA
* * * *
1103319 TGCCAATGTGCTGATTCAAGGCCAACAACATTGGTCTTA
1 TGCCAATATGCCGATTCAAAGCCAACAACATTGGGCTTA
1103358 AAGATGCCGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (39 bp):
TGCCAATATGCCGATTCAAAGCCAACAACATTGGGCTTA
Found at i:1103431 original size:42 final size:43
Alignment explanation
Indices: 1103228--1103448 Score: 130
Period size: 48 Copynumber: 5.0 Consensus size: 43
1103218 CTTAAAGATG
* * * *
1103228 AAAA-TGCCAATGTGCTGATTCAAGACCAGCGACATTGGTCTT
1 AAAAGTGCCAATATGCTGAGTCAAGGCCAGCGACATTGGACTT
* * * * * *
1103270 AAAGACAAGGTGCCAATATGCCGATTCAAAGCCAACGATATTGGGCTT
1 --A-A-AA-GTGCCAATATGCTGAGTCAAGGCCAGCGACATTGGACTT
* * * * *
1103318 ---A-TGCCAATGTGCTGATTCAAGGCCAACAACATTGGTCTT
1 AAAAGTGCCAATATGCTGAGTCAAGGCCAGCGACATTGGACTT
* * *
1103357 AAAGATGCCGATGCCAATATGCTGATTTAAGGCCAGTGACATT-GACTT
1 AAA-A----G-TGCCAATATGCTGAGTCAAGGCCAGCGACATTGGACTT
*
1103405 AAAAGTGCCAATATGCTGAGTCAAGGCCAGCGATATTGGACTT
1 AAAAGTGCCAATATGCTGAGTCAAGGCCAGCGACATTGGACTT
1103448 A
1 A
1103449 GAAGAAGATG
Statistics
Matches: 139, Mismatches: 23, Indels: 31
0.72 0.12 0.16
Matches are distributed among these distances:
39 32 0.23
41 1 0.01
42 28 0.20
43 8 0.06
44 1 0.01
45 1 0.01
46 2 0.01
47 1 0.01
48 38 0.27
49 27 0.19
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (43 bp):
AAAAGTGCCAATATGCTGAGTCAAGGCCAGCGACATTGGACTT
Found at i:1103535 original size:28 final size:29
Alignment explanation
Indices: 1103470--1103711 Score: 280
Period size: 29 Copynumber: 8.5 Consensus size: 29
1103460 CACCAACTTG
**
1103470 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGCTTTTGAAA-GGTTGCCACTGACT
* *
1103499 TATGTGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * *
1103527 TGTGGGCTTTTGAAAAGATACCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* *
1103556 TGTGGGC--TTGAAAGGGGTGCCATTGACT
1 TGTGGGCTTTTGAAA-GGTTGCCACTGACT
1103584 TGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * *
1103612 TGTGGGCTTTGGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
*
1103641 TGTGGGCTTTTG-AAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * *
1103669 TGTGGGCTTTGGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
1103698 TGTGGGCTTTTGAA
1 TGTGGGCTTTTGAA
1103712 GGTGAGGAAT
Statistics
Matches: 179, Mismatches: 27, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
27 11 0.06
28 82 0.46
29 83 0.46
30 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.33
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGTTGCCACTGACT
Found at i:1103600 original size:85 final size:84
Alignment explanation
Indices: 1103470--1103711 Score: 308
Period size: 85 Copynumber: 2.8 Consensus size: 84
1103460 CACCAACTTG
* * *
1103470 TGTGGGCTTTTGAAAGGGTTG-CACCAACTTATGTGCTTTTGAAGGTTGCCACTGACTTGTGGGC
1 TGTGGGC-TTTG-AAGGG-TGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
1103534 TTTTGAAAAGATACCACTGACT
63 TTTTGAAAAGATACCACTGACT
* *
1103556 TGTGGGC-TTGAAAGGGGTGCCATTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTG-AA-GGGTGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCT
* *
1103620 TTGGAAAAGATGCCACTGACT
64 TTTGAAAAGATACCACTGACT
* * * *
1103641 TGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCT
1 TGTGGGC-TTTGAAGGGTGCCACTAACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCT
1103706 TTTGAA
64 TTTGAA
1103712 GGTGAGGAAT
Statistics
Matches: 137, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
84 8 0.06
85 90 0.66
86 36 0.26
87 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.33
Consensus pattern (84 bp):
TGTGGGCTTTGAAGGGTGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT
TGAAAAGATACCACTGACT
Found at i:1103712 original size:57 final size:57
Alignment explanation
Indices: 1103470--1103714 Score: 300
Period size: 57 Copynumber: 4.3 Consensus size: 57
1103460 CACCAACTTG
* * * * * *
1103470 TGTGGGCTTTTGAAAGGGTTG-CACCAACTTATGTGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTG-AA-GGTTGCCACTAACTTGTGGGCTTTGGAAAAGATGCCACTGACT
* * * * * * *
1103527 TGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGC-TT-GAAAGGGGTGCCATTGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTAACTTGTGGGCTTTGGAAA-AGATGCCACTGACT
*
1103584 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGGAAAAGATGCCACTGACT
1103641 TGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGGAAAAGATGCCACTGACT
1103698 TGTGGGCTTTTGAAGGT
1 TGTGGGCTTTTGAAGGT
1103715 GAGGAATGTC
Statistics
Matches: 167, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
55 1 0.01
56 26 0.16
57 136 0.81
58 4 0.02
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (57 bp):
TGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGGAAAAGATGCCACTGACT
Found at i:1105142 original size:1 final size:1
Alignment explanation
Indices: 1105132--1105229 Score: 52
Period size: 1 Copynumber: 98.0 Consensus size: 1
1105122 ATCCGAACCC
* * * * ** * * * * * *
1105132 TTTTTGTTTTTTTTGTTTTATTTTATTTTGGTGTTTTTTGTTTATTTTGTTTTTTTTTGTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
1105197 TGTTTTTTTTCTTTTTTTTCTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1105230 GCGGAGGATG
Statistics
Matches: 67, Mismatches: 30, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.84
Consensus pattern (1 bp):
T
Found at i:1105146 original size:9 final size:9
Alignment explanation
Indices: 1105132--1105229 Score: 78
Period size: 9 Copynumber: 11.1 Consensus size: 9
1105122 ATCCGAACCC
1105132 TTTTTGTTT
1 TTTTTGTTT
1105141 TTTTTG-TT
1 TTTTTGTTT
* *
1105149 TTATT-TTA
1 TTTTTGTTT
* *
1105157 TTTTGGTGT
1 TTTTTGTTT
1105166 TTTTTGTTT
1 TTTTTGTTT
*
1105175 ATTTTGTTT
1 TTTTTGTTT
1105184 TTTTT-TGTT
1 TTTTTGT-TT
*
1105193 TGTTTGTTT
1 TTTTTGTTT
*
1105202 TTTTTCTTT
1 TTTTTGTTT
*
1105211 TTTTTCTTT
1 TTTTTGTTT
1105220 CTTTTT-TTT
1 -TTTTTGTTT
1105229 T
1 T
1105230 GCGGAGGATG
Statistics
Matches: 71, Mismatches: 13, Indels: 11
0.75 0.14 0.12
Matches are distributed among these distances:
8 12 0.17
9 53 0.75
10 6 0.08
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.84
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:1105170 original size:34 final size:34
Alignment explanation
Indices: 1105132--1105214 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 34
1105122 ATCCGAACCC
1105132 TTTTTGTTTTTTTTGTTTTATTTTAT-TTTG-GTGT
1 TTTTTGTTTTTTTTGTTTT-TTTT-TGTTTGTGTGT
* *
1105166 TTTTTGTTTATTTTGTTTTTTTTTGTTTGTTTGT
1 TTTTTGTTTTTTTTGTTTTTTTTTGTTTGTGTGT
*
1105200 TTTTTTTCTTTTTTT
1 TTTTTGT-TTTTTTT
1105215 TCTTTCTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 1 0.02
33 8 0.19
34 27 0.64
35 6 0.14
ACGTcount: A:0.04, C:0.01, G:0.12, T:0.83
Consensus pattern (34 bp):
TTTTTGTTTTTTTTGTTTTTTTTTGTTTGTGTGT
Found at i:1105187 original size:19 final size:19
Alignment explanation
Indices: 1105153--1105206 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
1105143 TTTGTTTTAT
* *
1105153 TTTATTTTGGTGTTTTTTG
1 TTTATTTTGTTTTTTTTTG
1105172 TTTATTTTGTTTTTTTTTG
1 TTTATTTTGTTTTTTTTTG
*
1105191 TTT-GTTTGTTTTTTTT
1 TTTATTTTGTTTTTTTT
1105207 CTTTTTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 12 0.38
19 20 0.62
ACGTcount: A:0.04, C:0.00, G:0.15, T:0.81
Consensus pattern (19 bp):
TTTATTTTGTTTTTTTTTG
Found at i:1111181 original size:19 final size:19
Alignment explanation
Indices: 1111157--1111224 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1111147 AATTCAACAA
1111157 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1111176 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1111191 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1111208 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1111225 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1111196 original size:13 final size:13
Alignment explanation
Indices: 1111178--1111202 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1111168 ACATAAGTTT
1111178 TGTATCGATACAA
1 TGTATCGATACAA
1111191 TGTATCGATACA
1 TGTATCGATACA
1111203 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1111200 original size:32 final size:32
Alignment explanation
Indices: 1111159--1111221 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1111149 TTCAACAATT
*
1111159 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1111191 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1111222 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1111282 original size:13 final size:13
Alignment explanation
Indices: 1111264--1111289 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1111254 CATTTTTCTG
1111264 TGTATCGATACAT
1 TGTATCGATACAT
1111277 TGTATCGATACAT
1 TGTATCGATACAT
1111290 GGATCTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1111543 original size:21 final size:21
Alignment explanation
Indices: 1111492--1111543 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
1111482 ATCACATTTT
*
1111492 GGTCCAAATGTATCGATACAT
1 GGTCCAAATGTATCGATACAA
* * *
1111513 TGTTCTAATGTATCGATACAA
1 GGTCCAAATGTATCGATACAA
*
1111534 GGTCCCAATG
1 GGTCCAAATG
1111544 GTCAAAAATT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (21 bp):
GGTCCAAATGTATCGATACAA
Found at i:1111626 original size:33 final size:33
Alignment explanation
Indices: 1111570--1111636 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1111560 TTCAACGATT
*
1111570 TGTATCGATACATAAAGTGTTGTATTGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1111603 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1111636 T
1 T
1111637 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1111679 original size:21 final size:21
Alignment explanation
Indices: 1111653--1111710 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
1111643 TACTGCCAAA
1111653 AAATGTATCGATACATCACTT
1 AAATGTATCGATACATCACTT
1111674 AAATGTATCGATACATCACTT
1 AAATGTATCGATACATCACTT
1111695 AAATGTATCGATACAT
1 AAATGTATCGATACAT
1111711 TGTATCGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
AAATGTATCGATACATCACTT
Found at i:1111716 original size:13 final size:13
Alignment explanation
Indices: 1111698--1111722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1111688 ATCACTTAAA
1111698 TGTATCGATACAT
1 TGTATCGATACAT
1111711 TGTATCGATACA
1 TGTATCGATACA
1111723 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1116617 original size:53 final size:52
Alignment explanation
Indices: 1116438--1116660 Score: 222
Period size: 52 Copynumber: 4.3 Consensus size: 52
1116428 TTATTTCTGA
* *** *
1116438 GGGGATACTCCAACCCC-GTCTTTATTTCC-AAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGGT-TTTATTTCCAAAAACACCAATTTTTCCTAATC
* * * *
1116489 GGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTTCC-TAATC
* *
1116541 GGGGATACTCTAACCCCGGTTTTATTTTC-AAAACACCAATTTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTTCC--TAATC
** * *
1116594 GGGGATACTCCAACTTCGATTTTATTTCCAAAAATACCAATTTTTCAC-AATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTTC-CTAATC
*
1116646 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1116661 TCGTTATCTC
Statistics
Matches: 146, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
50 3 0.02
51 34 0.23
52 62 0.42
53 31 0.21
54 15 0.10
55 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTTCCTAATC
Found at i:1116705 original size:28 final size:28
Alignment explanation
Indices: 1116648--1116719 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
1116638 TCACAATCGA
* **
1116648 GGATACTCCAACCTCGTTATCTCATCGG
1 GGATACTCCAACCCCGTTATCTCAGAGG
*
1116676 GGATACTCCAACCCCGTTA-CTTCCGAGG
1 GGATACTCCAACCCCGTTATC-TCAGAGG
*
1116704 GGATACTCCGACCCCG
1 GGATACTCCAACCCCG
1116720 GCTTTATTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.22
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATCTCAGAGG
Found at i:1129302 original size:21 final size:20
Alignment explanation
Indices: 1129276--1129323 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1129266 CCTTCTCTTC
1129276 AAAAAAAAGCAAAAAAAAAAA
1 AAAAAAAAG-AAAAAAAAAAA
* *
1129297 AAAAAAAAGAAACAAAACAA
1 AAAAAAAAGAAAAAAAAAAA
*
1129317 AGAAAAA
1 AAAAAAA
1129324 GGAGAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAAAAAA
Found at i:1129318 original size:13 final size:12
Alignment explanation
Indices: 1129277--1129321 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
1129267 CTTCTCTTCA
*
1129277 AAAAAAAGCAA-
1 AAAAAAAGAAAC
1129288 AAAAAAA-AAA-
1 AAAAAAAGAAAC
1129298 AAAAAAAGAAAC
1 AAAAAAAGAAAC
1129310 AAAACAAAGAAA
1 AAAA-AAAGAAA
1129322 AAGGAGAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 9 0.30
11 10 0.33
12 4 0.13
13 7 0.23
ACGTcount: A:0.87, C:0.07, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAC
Found at i:1130520 original size:59 final size:59
Alignment explanation
Indices: 1130307--1131257 Score: 1214
Period size: 59 Copynumber: 16.3 Consensus size: 59
1130297 TCTGATTTTT
* * * **
1130307 AGTCCTCAAAGAGCAGGATGCCTTTCCTTTTAAAAGCCC-CGACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTT-AAAGCCCAC-ACAAGTTGGTGGCACCTT-C
* **
1130368 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
1130427 TAGTCCTCAAAGAGCAGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 -AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * * * * *
1130487 AGTCCTTAACGAGCGGGATGCTTTTTCTCTTAAAGCCTACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
1130546 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
1130605 AGTCCTCAAAGAGCGGGATGCCTTTTCTATTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
1130664 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTT-
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
1130722 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
1130781 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
1130840 AATCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
1130899 AGTCCTCAAAGAGCAAGATG-CTTTTGC-CTTTCAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTT-CTC-TT-AAAGCCCACACAAGTTGGTGGCACCTTC
* * *
1130959 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTT-AAAGCCCACACAAGTTGGTGGCACC-TTC
* **
1131020 AGTCCCCAAAGAGCAGGAAC-CC--TT-TC--AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGG-ACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* **
1131075 AGTCCTCAAAGAGCAGGACACC--TT-TC--AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTT-C
*
1131130 AGTCCTCAAAGAGCAGGAC-AC----CTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACC-TTC
** * *
1131185 AGTCCTCAAAGAGCAGGACGCC--TT-TC--AAAGCCCACAGGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
1131240 AGTCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
1131258 TACACTTTAT
Statistics
Matches: 820, Mismatches: 50, Indels: 46
0.90 0.05 0.05
Matches are distributed among these distances:
53 2 0.00
54 5 0.01
55 179 0.22
56 3 0.00
57 2 0.00
58 62 0.08
59 357 0.44
60 155 0.19
61 54 0.07
62 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (59 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:1130800 original size:235 final size:237
Alignment explanation
Indices: 1130307--1131253 Score: 1264
Period size: 235 Copynumber: 4.1 Consensus size: 237
1130297 TCTGATTTTT
* * * **
1130307 AGTCCTCAAAGAGCAGGATGCCTTTCCTTTTAAAAGCCC-CGACAAGTTGGTGGCATTTTCCAGT
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTT-AAAGCCCAC-ACAAGTTGGTGGCACCTTCCAGT
**
1130371 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCA
64 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCA
* * *
1130436 AAGAGCAGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTTAACGAGC
128 AAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGC
* * * * *
1130501 GGGATGCTTTTTCTCTTAAAGCCTACACAAGTTGGTGGCACCTTC
193 AGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1130546 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
* * *
1130610 TCAAAGAGCGGGATGCCTTTTCTATTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG
66 TCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG
*
1130675 AGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTT-AGTCCTCAAAGAGCGGG
131 AGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGG
1130739 ACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
196 ACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
1130781 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAATCC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
*
1130845 TCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAG
66 TCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG
* *
1130910 AGCAAGATG-CTTTTGC-CTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGC
131 AGCAGGACGCCTTTT-CTC-TT-AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGC
* *
1130973 AGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
193 AGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTC
* * **
1131020 AGTCCCCAAAGAGCAGGAAC-CC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 AGTCCTCAAAGAGC-GGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTC
* **
1131079 CTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
65 CTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAA
*
1131139 AGAGCAGGAC-AC----CTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGC
129 AGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGC
** * *
1131199 AGGACGCC-TTTC----AAAGCCCACAGGAGTTGGTGGCACTTTTT
193 AGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
1131240 AGTCCTCAAAGAGC
1 AGTCCTCAAAGAGC
1131254 AGGATACACT
Statistics
Matches: 649, Mismatches: 45, Indels: 47
0.88 0.06 0.06
Matches are distributed among these distances:
220 37 0.06
225 29 0.04
226 26 0.04
227 1 0.00
230 24 0.04
231 19 0.03
234 35 0.05
235 208 0.32
236 84 0.13
237 83 0.13
238 52 0.08
239 47 0.07
240 4 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (237 bp):
AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
TCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG
AGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGG
ACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:1131100 original size:27 final size:27
Alignment explanation
Indices: 1131070--1131210 Score: 65
Period size: 28 Copynumber: 5.1 Consensus size: 27
1131060 TTGGTGGCAT
1131070 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
1131097 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
1131125 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
** * * * **
1131152 TCTTAAAGCCCACACAAGTTGGTGG-CACC
1 T-TTCCAGTCCTCA-AAG-AGCAGGACACC
*
1131181 TTT-CAGTCCTCAAAGAGCAGGACGCC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
1131207 TTTC
1 TTTC
1131211 AAAGCCCACA
Statistics
Matches: 76, Mismatches: 28, Indels: 20
0.61 0.23 0.16
Matches are distributed among these distances:
25 6 0.08
26 14 0.18
27 17 0.22
28 20 0.26
29 13 0.17
30 6 0.08
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:1132033 original size:19 final size:19
Alignment explanation
Indices: 1132009--1132076 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1131999 AATTCAATAA
1132009 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1132028 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1132043 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1132060 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1132077 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1132047 original size:32 final size:32
Alignment explanation
Indices: 1132011--1132073 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1132001 TTCAATAATT
*
1132011 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1132043 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1132074 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1132048 original size:13 final size:13
Alignment explanation
Indices: 1132030--1132054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1132020 ACATAAGTTT
1132030 TGTATCGATACAA
1 TGTATCGATACAA
1132043 TGTATCGATACA
1 TGTATCGATACA
1132055 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1132134 original size:13 final size:13
Alignment explanation
Indices: 1132116--1132141 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1132106 CATTTTTCTG
1132116 TGTATCGATACAT
1 TGTATCGATACAT
1132129 TGTATCGATACAT
1 TGTATCGATACAT
1132142 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1132138 original size:33 final size:33
Alignment explanation
Indices: 1132096--1132162 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1132086 GCCAAGGAAA
***
1132096 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1132129 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1132162 T
1 T
1132163 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1134676 original size:31 final size:28
Alignment explanation
Indices: 1134595--1134665 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 28
1134585 TCACAATCGA
* ***
1134595 GGATACTCCAACCCCGTTA-ATCATCGG
1 GGATACTCCAACCCCGTTATTTCCGAGG
1134622 GGATACTCCAACCCCGTTATTTCCGAGG
1 GGATACTCCAACCCCGTTATTTCCGAGG
*
1134650 GGATACTCGAACCCCG
1 GGATACTCCAACCCCG
1134666 ACTTTATTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 19 0.50
28 19 0.50
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATTTCCGAGG
Found at i:1134827 original size:53 final size:53
Alignment explanation
Indices: 1134650--1134870 Score: 229
Period size: 52 Copynumber: 4.2 Consensus size: 53
1134640 ATTTCCGAGG
* ** * *** *
1134650 GGATACTCGAACCCCGACTTTATTTCC-AAAATATTGATTTTT-CATAATC-A
1 GGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATCGA
* * * *
1134700 GGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCACAATCGG
1 -GGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATCGA
* *
1134753 GGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTTCCTTCAATCGA
1 GGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTTCC-ACAATCGA
* * *
1134806 GGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATCGA
1 GGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATCGA
1134858 GGATACTCCAACC
1 GGATACTCCAACC
1134871 TCGTTATCTC
Statistics
Matches: 145, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
50 3 0.02
51 31 0.21
52 63 0.43
53 34 0.23
54 14 0.10
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (53 bp):
GGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATCGA
Found at i:1134915 original size:28 final size:28
Alignment explanation
Indices: 1134858--1134921 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1134848 TCACAATCGA
* **
1134858 GGATACTCCAACCTCGTTATCTCATCGG
1 GGATACTCCAACCCCGTTATCTCAGAGG
*
1134886 GGATACTCCAACCCCGTTA-CTTCCGAGG
1 GGATACTCCAACCCCGTTATC-TCAGAGG
1134914 GGATACTC
1 GGATACTC
1134922 TGACCCCGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATCTCAGAGG
Found at i:1134948 original size:264 final size:262
Alignment explanation
Indices: 1134479--1134980 Score: 767
Period size: 264 Copynumber: 1.9 Consensus size: 262
1134469 TTCTCAATTC
* * * * * *
1134479 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTTAAGACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGA
1134544 TACTCCAACTCCAATTTTATTTCCAAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCC
66 TACTCCAACTCCAATTTTATTTCC-AAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCC
*
1134609 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCGAACCCCGACTTTATT
130 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCGAACCCCGACTTTATT
* *
1134674 TCCAAAATATTGATTTTTCATAATCAGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
195 CCCAAAATATTGATTTCTCATAATCAGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
1134739 TTT
260 TTT
*
1134742 TCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCCT-TCAATCGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAA-TTTT-CTAT-AATCGA
* * *
1134806 GGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTTTTCACAATCGAGGATACTCCAAC
63 GGATACTCCAACTCCAATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAAC
* * *
1134870 CTCGTTATCTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCTG-ACCCCGGCTT
128 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTC-GAACCCCGACTT
**
1134934 TATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
191 TATTCCCAAAATATTGATTTCTCATAATCAGGGATACTCCAACCCCG
1134981 TTATTTTCAA
Statistics
Matches: 216, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
263 83 0.38
264 99 0.46
265 34 0.16
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (262 bp):
TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGA
TACTCCAACTCCAATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCC
GTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCGAACCCCGACTTTATTC
CCAAAATATTGATTTCTCATAATCAGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
TT
Found at i:1142426 original size:19 final size:21
Alignment explanation
Indices: 1142382--1142434 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 21
1142372 TACAAGCCAA
1142382 TGTATCGATACATATTTTTTTG
1 TGTATCGATACATA-TTTTTTG
1142404 TGTATCGATACATA-TTTTT-
1 TGTATCGATACATATTTTTTG
1142423 TGTATCGATACA
1 TGTATCGATACA
1142435 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.39
20 5 0.16
22 14 0.45
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (21 bp):
TGTATCGATACATATTTTTTG
Found at i:1143648 original size:19 final size:19
Alignment explanation
Indices: 1143624--1143696 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
1143614 AGCGATACAT
*
1143624 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
1143643 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
* ** *
1143662 TGTATTGATACATTTACTGTT
1 TGTATCGATACA-AAACT-TA
1143683 TGTATCGATACAAA
1 TGTATCGATACAAA
1143697 TTGTTGAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
19 29 0.66
20 3 0.07
21 12 0.27
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1150298 original size:79 final size:79
Alignment explanation
Indices: 1150158--1150304 Score: 181
Period size: 79 Copynumber: 1.9 Consensus size: 79
1150148 AATAAGGCAA
* *
1150158 GGGTTGAAGTGTCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAATCGAGATTTGAGTATCC
1 GGGTTGAAGTATCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAATCGAGATTGGAGTATCC
1150223 CCGTGAAAATAACG
66 CCGTGAAAATAACG
* * * *** *
1150237 GGGTTGAAGTATCCCCGATTGT-GAAAATTCGGTGTTTTGGAAATAAAATAG-GAGTTGGAGTAT
1 GGGTTGAAGTATCCCCGATTATAGAAAA-TAGATGTTTCAAAAATAAAATCGAGA-TTGGAGTAT
1150300 CCCCG
64 CCCCG
1150305 ATTAAGAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
78 7 0.12
79 50 0.88
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (79 bp):
GGGTTGAAGTATCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAATCGAGATTGGAGTATCC
CCGTGAAAATAACG
Found at i:1150361 original size:130 final size:129
Alignment explanation
Indices: 1150082--1150351 Score: 284
Period size: 130 Copynumber: 2.1 Consensus size: 129
1150072 TAATAATGGG
*
1150082 TTGGAGTAT-CCC-TCGAAAATAACGGGGCTGGAGTACCCCCCGATTGTGAAAAATCGATGATTT
1 TTGGAGTATCCCCGT-GAAAATAACGGGGCTGAAGTACCCCCCGATTGTGAAAAATCGATGATTT
* *
1150145 AGAAATAAGGCAAGGGTTGAAGTGTCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAATCGA
65 AGAAATAA-GAAAGGGTTGAAGTATCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAATC-A
*
1150210 GA
128 CA
* * * * * * *
1150212 TTTGAGTATCCCCGTGAAAATAACGGGGTTGAAGTA-TCCCCGATTGTGAAAATTCGGTGTTTTG
1 TTGGAGTATCCCCGTGAAAATAACGGGGCTGAAGTACCCCCCGATTGTGAAAAATCGATGATTTA
* * *** *
1150276 GAAATAA-AATAGGAGTTGGAGTATCCCCGATTA-AGAAAAATTGATGTTTTGGAAATGAAA-C-
66 GAAATAAGAA-AGG-GTTGAAGTATCCCCGATTATAG-AAAATAGATGTTTCAAAAATAAAATCA
1150337 CA
128 CA
1150339 TTGGAGTATCCCC
1 TTGGAGTATCCCC
1150352 AGGATGAAAA
Statistics
Matches: 117, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
127 13 0.11
128 1 0.01
129 6 0.05
130 74 0.63
131 22 0.19
132 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (129 bp):
TTGGAGTATCCCCGTGAAAATAACGGGGCTGAAGTACCCCCCGATTGTGAAAAATCGATGATTTA
GAAATAAGAAAGGGTTGAAGTATCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAATCACA
Found at i:1156609 original size:13 final size:13
Alignment explanation
Indices: 1156591--1156616 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1156581 ACATTTAGTG
1156591 ATGTATCGATACA
1 ATGTATCGATACA
1156604 ATGTATCGATACA
1 ATGTATCGATACA
1156617 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1156633 original size:32 final size:33
Alignment explanation
Indices: 1156569--1156636 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1156559 CGTTACAAGC
*
1156569 CAATGTATTGATACATTTAGTGATGTATCGATA
1 CAATGTATCGATACATTTAGTGATGTATCGATA
1156602 CAATGTATCGATACATATT-GTG-TGTATCGATA
1 CAATGTATCGATACAT-TTAGTGATGTATCGATA
1156634 CAA
1 CAA
1156637 ATTTAGCTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATTTAGTGATGTATCGATA
Found at i:1156694 original size:20 final size:20
Alignment explanation
Indices: 1156669--1156721 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1156659 CCAATGACTT
**
1156669 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
1156689 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
1156709 GTATCGATACATT
1 GTATCGATACATT
1156722 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:1157313 original size:22 final size:22
Alignment explanation
Indices: 1157286--1157330 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1157276 TTTTCTTTTC
1157286 TCTCCCCCTTAATCAAAA-AATT
1 TCTCCCCCTTAAT-AAAATAATT
1157308 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAATAATT
1157330 T
1 T
1157331 AACAATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAATAATT
Found at i:1158768 original size:21 final size:21
Alignment explanation
Indices: 1158737--1158788 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
1158727 GCTGCTAGTG
*
1158737 TGGGGGCTGCCCGGTTACGACC
1 TGGGGG-TGCCCGGTCACGACC
*
1158759 TGGGGGTG-CCGGTCGCGACC
1 TGGGGGTGCCCGGTCACGACC
1158779 TGGTGGGTGC
1 TGG-GGGTGC
1158789 TGCCTAGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 13 0.50
21 7 0.27
22 6 0.23
ACGTcount: A:0.06, C:0.27, G:0.48, T:0.19
Consensus pattern (21 bp):
TGGGGGTGCCCGGTCACGACC
Found at i:1159227 original size:13 final size:13
Alignment explanation
Indices: 1159209--1159246 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1159199 ATAAACCCCT
*
1159209 TGTATCGATACAC
1 TGTATCGATACAA
1159222 TGTATCGATACAA
1 TGTATCGATACAA
1159235 TGTATCGATACA
1 TGTATCGATACA
1159247 GAGAATGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1166162 original size:13 final size:13
Alignment explanation
Indices: 1166144--1166169 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1166134 CAATTTTTTG
1166144 TGTATCGATACAT
1 TGTATCGATACAT
1166157 TGTATCGATACAT
1 TGTATCGATACAT
1166170 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1166910 original size:21 final size:21
Alignment explanation
Indices: 1166869--1166912 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1166859 CTCTCCTTTA
* *
1166869 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1166890 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1166911 TC
1 TC
1166913 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1166930 original size:34 final size:34
Alignment explanation
Indices: 1166887--1166958 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
1166877 GTTTATTAAT
1166887 AATTCTCCCCCTTAATCAAGTAATTCATATAAAA
1 AATTCTCCCCCTTAATCAAGTAATTCATATAAAA
*
1166921 AATTCTCCCCCTTAATCAAGTAATTCATATCAAA
1 AATTCTCCCCCTTAATCAAGTAATTCATATAAAA
1166955 AATT
1 AATT
1166959 TATTTGCACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.33
Consensus pattern (34 bp):
AATTCTCCCCCTTAATCAAGTAATTCATATAAAA
Found at i:1168772 original size:13 final size:13
Alignment explanation
Indices: 1168754--1168779 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1168744 ATAATCACCC
1168754 TGTATCGATACAA
1 TGTATCGATACAA
1168767 TGTATCGATACAA
1 TGTATCGATACAA
1168780 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1172720 original size:21 final size:21
Alignment explanation
Indices: 1172691--1172735 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1172681 AAGTTTTCAT
*
1172691 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1172711 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1172733 TTT
1 TTT
1172736 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1174978 original size:13 final size:13
Alignment explanation
Indices: 1174960--1174985 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1174950 ACAATTTTTG
1174960 TGTATCGATACAT
1 TGTATCGATACAT
1174973 TGTATCGATACAT
1 TGTATCGATACAT
1174986 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1174982 original size:32 final size:32
Alignment explanation
Indices: 1174941--1175003 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1174931 TACAAGCTAA
**
1174941 TGTATCGATACAATTTTTG-TGTATCGATACAT
1 TGTATCGATAC-ATACTTGCTGTATCGATACAT
1174973 TGTATCGATACATACTTGCTGTATCGATACA
1 TGTATCGATACATACTTGCTGTATCGATACA
1175004 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATACTTGCTGTATCGATACAT
Found at i:1175460 original size:20 final size:20
Alignment explanation
Indices: 1175435--1175487 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1175425 CCAATGGCTT
**
1175435 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
1175455 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
*
1175475 GTATCAATACATT
1 GTATCGATACATT
1175488 GTATCGATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:1178389 original size:20 final size:21
Alignment explanation
Indices: 1178345--1178391 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
1178335 CATTACTAAA
1178345 TGTATCAATACATGTTTACCAT
1 TGTATCAATACATGTTTA-CAT
1178367 TGTATCAATACAT-TTCT-CAT
1 TGTATCAATACATGTT-TACAT
1178387 TGTAT
1 TGTAT
1178392 TGATATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.33
21 2 0.08
22 14 0.58
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.45
Consensus pattern (21 bp):
TGTATCAATACATGTTTACAT
Found at i:1179569 original size:19 final size:18
Alignment explanation
Indices: 1179545--1179586 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1179535 CCCCTTTTTT
1179545 TTAAAATAAA-AAGTCCAAA
1 TTAAAA-AAATAAG-CCAAA
*
1179564 TTAAAAAAATAAGCCCAA
1 TTAAAAAAATAAGCCAAA
1179582 TTAAA
1 TTAAA
1179587 TCGGATCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.21
Consensus pattern (18 bp):
TTAAAAAAATAAGCCAAA
Found at i:1180891 original size:13 final size:13
Alignment explanation
Indices: 1180873--1180944 Score: 144
Period size: 13 Copynumber: 5.5 Consensus size: 13
1180863 ACATAAGTGT
1180873 TGTATCGATACAA
1 TGTATCGATACAA
1180886 TGTATCGATACAA
1 TGTATCGATACAA
1180899 TGTATCGATACAA
1 TGTATCGATACAA
1180912 TGTATCGATACAA
1 TGTATCGATACAA
1180925 TGTATCGATACAA
1 TGTATCGATACAA
1180938 TGTATCG
1 TGTATCG
1180945 CTACGAAGCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 59 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1181007 original size:13 final size:13
Alignment explanation
Indices: 1180989--1181016 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1180979 ATTACTCAAA
1180989 TGTATCGATACAT
1 TGTATCGATACAT
1181002 TGTATCGATACAT
1 TGTATCGATACAT
1181015 TG
1 TG
1181017 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1185744 original size:13 final size:13
Alignment explanation
Indices: 1185726--1185751 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1185716 CAATTTTTTG
1185726 TGTATCGATACAT
1 TGTATCGATACAT
1185739 TGTATCGATACAT
1 TGTATCGATACAT
1185752 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1185763 original size:32 final size:33
Alignment explanation
Indices: 1185706--1185769 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1185696 TACAAGCCAA
**
1185706 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1185739 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1185770 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1188746 original size:84 final size:84
Alignment explanation
Indices: 1188591--1188755 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
1188581 CATTTTCCAC
* * * *
1188591 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
1188656 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
1188675 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
1188737 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
1188756 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 54 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:1190821 original size:13 final size:13
Alignment explanation
Indices: 1190803--1190828 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1190793 CAATTTTTTG
1190803 TGTATCGATACAT
1 TGTATCGATACAT
1190816 TGTATCGATACAT
1 TGTATCGATACAT
1190829 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1190840 original size:32 final size:33
Alignment explanation
Indices: 1190783--1190846 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1190773 TACAAGCCAA
**
1190783 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1190816 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1190847 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1198022 original size:155 final size:155
Alignment explanation
Indices: 1197824--1198235 Score: 481
Period size: 155 Copynumber: 2.7 Consensus size: 155
1197814 CCACCTTTAA
* * * * * *
1197824 CATAAAAGCGGACCTGACGACAACCTAGGAGTTGATTTTGAAAAATTACGAAAATACCTCT-GGA
1 CATAAAAGCGAACCTGATGACAACTTAGGACTCGATTTTGAAAAATTACGAAAATGCCTCTAGGA
1197888 GCATACCTTTGACGTAAAAGTACTCGATACCCCTAAAGAACCTAAAAAGGATAATAGATAGGATG
66 G-ATACCTTTGACGTAAAAGTACTCGATACCCCTAAAGAACCTAAAAAGGATAATAGATAGGATG
* *
1197953 AAACTATCCTTAATATCTAATTTCGG
130 AAACTATCATTAATATCTAACTTCGG
* * * * *
1197979 CATAAAAGCGAACCTGATGATAACTTAGGACTCGGTTCTGAAAAATTACGAAAATGCTTTTAAGG
1 CATAAAAGCGAACCTGATGACAACTTAGGACTCGATTTTGAAAAATTACGAAAATGCCTCT-AGG
* *
1198044 -GATA-CTTTCGACGTAAAAGTAC-CTGATACCCCTAAAGAACTTAAAAAGGATAATAGATGGGA
65 AGATACCTTT-GACGTAAAAGTACTC-GATACCCCTAAAGAACCTAAAAAGGATAATAGATAGGA
* *
1198106 TGAACCTATCATTAATATCTACCTTCGG
128 TGAAACTATCATTAATATCTAACTTCGG
* * * * * * * * *
1198134 CATAGAAGCAAACCCGGTGACAACTTAGGACTCGATTTTAAAAAAATATGAAAATGCCCCTAGAA
1 CATAAAAGCGAACCTGATGACAACTTAGGACTCGATTTTGAAAAATTACGAAAATGCCTCTAGGA
* * * **
1198199 GATACATTTGACATAAAAGTACTTGACGCCCCTAAAG
66 GATACCTTTGACGTAAAAGTACTCGATACCCCTAAAG
1198236 GACTTGGGAT
Statistics
Matches: 214, Mismatches: 36, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
154 7 0.03
155 201 0.94
156 4 0.02
157 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (155 bp):
CATAAAAGCGAACCTGATGACAACTTAGGACTCGATTTTGAAAAATTACGAAAATGCCTCTAGGA
GATACCTTTGACGTAAAAGTACTCGATACCCCTAAAGAACCTAAAAAGGATAATAGATAGGATGA
AACTATCATTAATATCTAACTTCGG
Found at i:1198867 original size:156 final size:155
Alignment explanation
Indices: 1198509--1198979 Score: 586
Period size: 156 Copynumber: 3.0 Consensus size: 155
1198499 ATTTTCTTGA
* * * *
1198509 AAATATTAATTCAATTTAATTTAATTTATTTTTAAAAATACCATTTCGTACCTTAATAGAAGCCT
1 AAATATTAATTCAATTTAATTTTATTTATTTTTAAAAATACAATTTCGTACCTTAATGGAAGCCC
* * *
1198574 AAAAGAATACGAAAGATTTTTTTGAAAATC-TTTATA-CCCTACGGATGCCCATAGGAATATAAA
66 AAAAGGATACGAAA-ATGTTTTT-AAAATCTTTTATACCCCTACGGATGCCTATAGGAATATAAA
*
1198637 AGATTAGAAAAAATAGATATTAGAATTTATTCCG
129 AGATTA-AAAAAAT---TA--A-AATTTAATCCG
** * * * *
1198671 ATAATACCAATTTAATTTAATTTTATTTATTTTTGAAAATACAATTTTGTACCCTAATGGAAGCC
1 A-AATATTAATTCAATTTAATTTTATTTATTTTTAAAAATACAATTTCGTACCTTAATGGAAGCC
* * * *
1198736 CGAAAGGATACGAAAACGTTTTTAAAATCTTTTATACCCCTATGGATGCTTATAGGAATATAAAA
65 CAAAAGGATACGAAAATGTTTTTAAAATCTTTTATACCCCTACGGATGCCTATAGGAATATAAAA
1198801 GATTAAAAAAATTAAAATTTAATCCG
130 GATTAAAAAAATTAAAATTTAATCCG
* *
1198827 AAAGTATTAATTCAATTTAATTTTATTTATTTTTAAAAATACTATTTCGTACCTTAATGGAAACC
1 AAA-TATTAATTCAATTTAATTTTATTTATTTTTAAAAATACAATTTCGTACCTTAATGGAAGCC
* * * **
1198892 CTAAAGGATACGAAAATGTTTTTAAAATCTTTTACACCCTTACAAATGCCTATAGGAATATAAAA
65 CAAAAGGATACGAAAATGTTTTTAAAATCTTTTATACCCCTACGGATGCCTATAGGAATATAAAA
* *
1198957 AATGAAAAAAATTAAAATTTAAT
130 GATTAAAAAAATTAAAATTTAAT
1198980 TTCATCACTA
Statistics
Matches: 269, Mismatches: 36, Indels: 14
0.84 0.11 0.04
Matches are distributed among these distances:
155 2 0.01
156 142 0.53
157 1 0.00
159 2 0.01
161 6 0.02
162 20 0.07
163 96 0.36
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (155 bp):
AAATATTAATTCAATTTAATTTTATTTATTTTTAAAAATACAATTTCGTACCTTAATGGAAGCCC
AAAAGGATACGAAAATGTTTTTAAAATCTTTTATACCCCTACGGATGCCTATAGGAATATAAAAG
ATTAAAAAAATTAAAATTTAATCCG
Found at i:1199918 original size:29 final size:28
Alignment explanation
Indices: 1199877--1199945 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
1199867 ACTAGCCTAG
*
1199877 CTTTTCTATTTTT-TTTCTATATTTTCTT
1 CTTTTCTTTTTTTCTTTCTATATTTTC-T
* *
1199905 CTTTTTCTTTTTTTCTTTCTCTCTTTTCT
1 C-TTTTCTTTTTTTCTTTCTATATTTTCT
*
1199934 CTCTTCTTTTTT
1 CTTTTCTTTTTT
1199946 GTTGAACTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 11 0.31
29 13 0.37
30 11 0.31
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.75
Consensus pattern (28 bp):
CTTTTCTTTTTTTCTTTCTATATTTTCT
Found at i:1200628 original size:166 final size:163
Alignment explanation
Indices: 1200411--1200913 Score: 518
Period size: 163 Copynumber: 3.1 Consensus size: 163
1200401 TCAACATATA
* *
1200411 CAAAAAAAATTCAAAATTAAT-GAAATAAATTAAAATTTTCAAAAATGAATTAAT-T-AAAGTTT
1 CAAAAAAAATTCAAAATTAATGGAAATAAA-TAAAATTTTGAAAACTGAATTAATATGAAA--TT
* * * * ** * * * *
1200473 AATGACAATATTAGATGAATTTTAAAAATTTTAAATCGAGAAAAATTCTCTCGAAAAAATTTATG
63 AATAATAATATTTGATGACTTTTAAAAATTAAAAAACAAGAAAAA-TCCCTCGAAAAAATTTACG
* * *
1200538 TAGTAAAAAACTCGATTTTTTGGAAAAATGAG-ATTT
127 AAGTAAAAAACTCGATTTTTTCGAAAAAAGAGAATTT
* * * *
1200574 CAAGGAAAAAAATTCAAAATTCATGGAAATTAATGAATTTTTGAAAACTGAATTAATATGAAATT
1 C-A--AAAAAAATTCAAAATTAATGGAAATAAATAAAATTTTGAAAACTGAATTAATATGAAATT
* * *
1200639 AATAATAATATTTGATTACTTTTAAAAATTAAAAAACAAGAAAAATCCCGCTGAAAGAATTTACG
63 AATAATAATATTTGATGACTTTTAAAAATTAAAAAACAAGAAAAATCCCTC-GAAAAAATTTACG
* *
1200704 AAGT-AAAAACTCCA-TATTTCGAAAAAAGAGAAATTT
127 AAGTAAAAAACTCGATTTTTTCGAAAAAAGAG-AATTT
* * * * * *
1200740 CAAAAAAAATTCAAAATTTATGGAAATGAATAAACTTTTGAACACTAAATTAATATGAAATAAAT
1 CAAAAAAAATTCAAAATTAATGGAAATAAATAAAATTTTGAAAACTGAATTAATATGAAATTAAT
* *
1200805 AATAATATTTGATGACTTTTAAAAATTAAAAAACAAGAAAAATCCCTTTGAAAAAATTTACGGAG
66 AATAATATTTGATGACTTTTAAAAATTAAAAAACAAGAAAAATCCC-TCGAAAAAATTTACGAAG
* * *
1200870 TAAAAAACTTCG-TATTTT-GAAAAAAAGAAAACTT
130 TAAAAAAC-TCGATTTTTTCG-AAAAAAGAGAATTT
*
1200904 CAAGAAAAAT
1 CAAAAAAAAT
1200914 AAAAAAATTC
Statistics
Matches: 284, Mismatches: 42, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
163 117 0.41
164 34 0.12
165 27 0.10
166 95 0.33
167 8 0.03
168 3 0.01
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (163 bp):
CAAAAAAAATTCAAAATTAATGGAAATAAATAAAATTTTGAAAACTGAATTAATATGAAATTAAT
AATAATATTTGATGACTTTTAAAAATTAAAAAACAAGAAAAATCCCTCGAAAAAATTTACGAAGT
AAAAAACTCGATTTTTTCGAAAAAAGAGAATTT
Found at i:1200919 original size:19 final size:19
Alignment explanation
Indices: 1200888--1200929 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1200878 TTCGTATTTT
*
1200888 GAAAAAAAGAAAACTTCAA
1 GAAAAAAAGAAAAATTCAA
*
1200907 GAAAAATAA-AAAAATTCAT
1 GAAAAA-AAGAAAAATTCAA
1200926 GAAA
1 GAAA
1200930 TTTAAAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.69, C:0.07, G:0.10, T:0.14
Consensus pattern (19 bp):
GAAAAAAAGAAAAATTCAA
Found at i:1204602 original size:29 final size:28
Alignment explanation
Indices: 1204542--1204607 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 28
1204532 TAAAGTAAAC
*
1204542 TTTATATTTTTATTGTGTTCAAATAAATT
1 TTTAT-TTTTTATTGTATTCAAATAAATT
1204571 TTTATTTTTTAATTTGTATTCAAATAAATT
1 TTTATTTTTT-A-TTGTATTCAAATAAATT
1204601 TTTATTT
1 TTTATTT
1204608 CAAATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 5 0.15
29 6 0.18
30 23 0.68
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (28 bp):
TTTATTTTTTATTGTATTCAAATAAATT
Found at i:1204654 original size:23 final size:23
Alignment explanation
Indices: 1204628--1204679 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1204618 ATTAATTTAT
1204628 ATTAAAAGT-TTATTTAAACATAA
1 ATTAAAA-TATTATTTAAACATAA
*
1204651 ATTAAAATATTATTTAAATATAA
1 ATTAAAATATTATTTAAACATAA
1204674 ATTAAA
1 ATTAAA
1204680 TGTTAAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTAAAATATTATTTAAACATAA
Found at i:1208608 original size:19 final size:19
Alignment explanation
Indices: 1208581--1208623 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1208571 TTTATCAATA
* *
1208581 AAAAGTTTGTATCAAACCC
1 AAAATTTTGAATCAAACCC
1208600 AAAATTTTGAATCAAACCC
1 AAAATTTTGAATCAAACCC
1208619 AAAAT
1 AAAAT
1208624 CGCTGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.19, G:0.07, T:0.26
Consensus pattern (19 bp):
AAAATTTTGAATCAAACCC
Found at i:1209130 original size:22 final size:20
Alignment explanation
Indices: 1209102--1209141 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1209092 AAAATATTTT
1209102 ATTATTTTTTAAAATAATTACC
1 ATTA-TTTTTAAAA-AATTACC
1209124 ATTATTTTTAAAAAATTA
1 ATTATTTTTAAAAAATTA
1209142 TGATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATTTTTAAAAAATTACC
Found at i:1209528 original size:16 final size:17
Alignment explanation
Indices: 1209494--1209532 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1209484 ATTTATTTGT
*
1209494 ATTTGAATTAGAATATA
1 ATTTGAATTAAAATATA
*
1209511 ATTT-AATTAAAATTTA
1 ATTTGAATTAAAATATA
1209527 ATTTGA
1 ATTTGA
1209533 TAGTAATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (17 bp):
ATTTGAATTAAAATATA
Found at i:1211679 original size:109 final size:113
Alignment explanation
Indices: 1211484--1211811 Score: 350
Period size: 109 Copynumber: 2.9 Consensus size: 113
1211474 TGTAATTTAT
* * *
1211484 TTAA-TTAAGGCTAAGTCTTATAAAAATATATATTA-ACTAAAATAGAT-CTCACATGCTTATTT
1 TTAACTTAAGGCCAAGTCTTATAAAAATATATATTAGA-TAAAATAGGTGCTCACGTGCTTATTT
*
1211546 AATTAATTTA-TCTAGGCCTATTTTATTTAATTATATTGGGTCAT-AA-A
65 AATTAATTTATTCTA-GCTTATTTTATTTAATTATATTGGGTCATAAATA
* *
1211593 -TAACTTAAGGCCAAATCTTATAAAAATATATATTAGATAAAATAGGTGC-CACGTGTTTATTTA
1 TTAACTTAAGGCCAAGTCTTATAAAAATATATATTAGATAAAATAGGTGCTCACGTGCTTATTTA
* * * * *
1211656 ATTAATATATTTTAGCTTATTTTATTTAATTATATTAGATTATAAATTA
66 ATTAATTTATTCTAGCTTATTTTATTTAATTATATTGGGTCATAAA-TA
* ** * * *
1211705 TTTAATTTAAGATCAAGCCTTATAAAAGGATATATATTAGATAAAATAGG-GCTTACGTGCATAT
1 -TTAACTTAAGGCCAAGTCTTATAAAA--ATATATATTAGATAAAATAGGTGCTCACGTGCTTAT
* * *
1211769 TTAATTAATTTATTCGAGATTTATTTTATTTAATTATGTTGGG
63 TTAATTAATTTATTCTAG-CTTATTTTATTTAATTATATTGGG
1211812 CTAATTTTTA
Statistics
Matches: 180, Mismatches: 26, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
108 3 0.02
109 83 0.46
110 7 0.04
112 1 0.01
114 20 0.11
115 2 0.01
116 44 0.24
117 20 0.11
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (113 bp):
TTAACTTAAGGCCAAGTCTTATAAAAATATATATTAGATAAAATAGGTGCTCACGTGCTTATTTA
ATTAATTTATTCTAGCTTATTTTATTTAATTATATTGGGTCATAAATA
Found at i:1211693 original size:23 final size:24
Alignment explanation
Indices: 1211652--1211698 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1211642 CACGTGTTTA
* *
1211652 TTTAATTAATATATTTTAGCTTAT
1 TTTAATTAATATATATTAGATTAT
*
1211676 TTTATTTAAT-TATATTAGATTAT
1 TTTAATTAATATATATTAGATTAT
1211699 AAATTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTAATTAATATATATTAGATTAT
Found at i:1212878 original size:21 final size:24
Alignment explanation
Indices: 1212842--1212884 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
1212832 AGTATAAATG
1212842 TTTTCAAGGCTTAAAAT-TATCGA
1 TTTTCAAGGCTTAAAATATATCGA
1212865 TTTTCAA-G-TTAAAATATATC
1 TTTTCAAGGCTTAAAATATATC
1212885 AAAGTATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (24 bp):
TTTTCAAGGCTTAAAATATATCGA
Found at i:1213017 original size:13 final size:13
Alignment explanation
Indices: 1212999--1213023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1212989 ATATTGCATA
1212999 GTATCGATACATT
1 GTATCGATACATT
1213012 GTATCGATACAT
1 GTATCGATACAT
1213024 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1213141 original size:13 final size:13
Alignment explanation
Indices: 1213123--1213148 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1213113 TATACACAAG
1213123 ATGTATCGATACA
1 ATGTATCGATACA
1213136 ATGTATCGATACA
1 ATGTATCGATACA
1213149 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1213165 original size:33 final size:32
Alignment explanation
Indices: 1213105--1213168 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1213095 CTTAACTGTT
* *
1213105 TGTATCGATATACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
1213137 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
1213169 TTAGCTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:1219379 original size:20 final size:20
Alignment explanation
Indices: 1219344--1219385 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
1219334 CAAATTTCTT
1219344 ATTTTTCACTTCAAAATACATC
1 ATTTTTCAC-TCAAAAT-CATC
1219366 ATTTTTCA-TCAAAATCATC
1 ATTTTTCACTCAAAATCATC
1219385 A
1 A
1219386 ACAAAAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTTTCACTCAAAATCATC
Found at i:1221711 original size:13 final size:13
Alignment explanation
Indices: 1221693--1221717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1221683 ATATTGCACA
1221693 GTATCGATACATT
1 GTATCGATACATT
1221706 GTATCGATACAT
1 GTATCGATACAT
1221718 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1221824 original size:13 final size:13
Alignment explanation
Indices: 1221806--1221831 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1221796 TATACACAAG
1221806 ATGTATCGATACA
1 ATGTATCGATACA
1221819 ATGTATCGATACA
1 ATGTATCGATACA
1221832 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1221848 original size:33 final size:32
Alignment explanation
Indices: 1221788--1221851 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1221778 CTTAACTGTT
* *
1221788 TGTATCGATATACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
1221820 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
1221852 TTGGCTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:1223422 original size:16 final size:16
Alignment explanation
Indices: 1223401--1223431 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1223391 TCGAAAAGGA
1223401 AGACCCTAATTGTCAT
1 AGACCCTAATTGTCAT
1223417 AGACCCTAATTGTCA
1 AGACCCTAATTGTCA
1223432 GATATTCGTG
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:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (16 bp):
AGACCCTAATTGTCAT
Found at i:1224047 original size:634 final size:633
Alignment explanation
Indices: 1222780--1224671 Score: 3327
Period size: 634 Copynumber: 3.0 Consensus size: 633
1222770 GATTCCACTA
* *
1222780 TCATAGACCCTAATTGTCAGATATTCGTGTGTCCAACACCTTGATATGCGTCTAG-AGGACCTAG
1 TCATAGACCCTAATTGTCAGATATTCGTGTGTCCAACACCTTGATATGTGTCTAGAAAGACCTAG
*
1222844 ACCCAAAAAACCCCTTGTTTGGTATTGGTGACATTTTGACCCTAAATTGAAAAATTATTTAAGAA
66 ACCCAAAAAACCCCTTGTTTGGTATTGGTGACATTTTGACCCCAAATTGAAAAATTATTTAAGAA
1222909 CTCTAGACGATTTTTATGGAATTTTATGATATTTTCTCTCAAAGGGTATCGAATTATCTATCTAA
131 CTCTAGACGATTTTTATGGAATTTTATGATATTTTCTCTCAAA-GGTATCGAATTATCTATCTAA
* *
1222974 TGGTATCTCATGTGCCCTTAGATGTGCTCAGATAAGAGAGTTATAATTTTTCAAACTTTCATTAT
195 TGGTATCTCATTTGCCCTTAGATGTGCTCAGATGAGAGAGTTATAATTTTTCAAACTTTCATTAT
* *
1223039 CTGGTACCCTTGGAATTAGCAATTAATATTTTATTTGGGCTGTTTTGGCCCATTAGCTGACTTTT
260 CTGGTACCCTTGGAATTAGCAATTAACATTTTATTTGGGTTGTTTTGGCCCATTAGCTGACTTTT
1223104 CTGAAATTTTTAAATATTTTTCCTATAAACTATATGAAATTCCCTTTCTAGAAAAGTATGATTTG
325 CTGAAATTTTTAAATATTTTTCCTATAAACTATATGAAATTCCCTTTCTAGAAAAGTATGATTTG
1223169 AGATTTAATGATTCCAAATGAGTTCAGAATGATTTTTTAAATTTTACTGCACCCTCTCCCTTGTA
390 AGATTTAATGATTCCAAATGAGTTCAGAATGATTTTTTAAATTTTACTGCACCCTCTCCCTTGTA
*
1223234 TTGGCTGTTAGTGTCGAACCAAATTTGATTTCAACAATTTTCTCCTAGAACAAGACTTTTTGGGA
455 TTGGCTGTTAGTGCCGAACCAAATTTGATTTCAACAATTTTCTCCTAGAACAAGACTTTTTGGGA
* *
1223299 TTTTTAGAATATTTTTTTATTAATTCTCATTGAGTTACCATTCCAAAAATACCTCGTTCTCACTA
520 TTTTTAGAATATTTTCTTATTAATTCTCATTGAGTTACCATTCCAACAATACCTCGTTCTCACTA
1223364 GAAGCTTTTAGATGAGCCGAAATAAACTCGAAAAGGAAGACCCTAATTG
585 GAAGCTTTTAGATGAGCCGAAATAAACTCGAAAAGGAAGACCCTAATTG
1223413 TCATAGACCCTAATTGTCAGATATTCGTGTGTCCAACACCTTGATATGTGTCTAGAAAGACCTAG
1 TCATAGACCCTAATTGTCAGATATTCGTGTGTCCAACACCTTGATATGTGTCTAGAAAGACCTAG
*
1223478 ACCCAAAAAACCCCTTCTTTGGTATTGGTGACATTTTGACCCCAAATTGAAAAATTATTTAAGAA
66 ACCCAAAAAACCCCTTGTTTGGTATTGGTGACATTTTGACCCCAAATTGAAAAATTATTTAAGAA
*
1223543 CTCTAGACGATTTTTATGGAATTTTATGATATTTTCTCTCAAAGTGTATCAAATTATCTATCTAA
131 CTCTAGACGATTTTTATGGAATTTTATGATATTTTCTCTCAAAG-GTATCGAATTATCTATCTAA
**
1223608 TGGTATCTCATTTGCCCTTAGATGTGCTCAGATGAGAGAGTTATAATTTTTTGAACTTTCATTAT
195 TGGTATCTCATTTGCCCTTAGATGTGCTCAGATGAGAGAGTTATAATTTTTCAAACTTTCATTAT
** *
1223673 CTGGTACATTTGGAATTAGCAATTAACATTTTATTTGGGTTGTTTTAGCCCATTAGCTGACTTTT
260 CTGGTACCCTTGGAATTAGCAATTAACATTTTATTTGGGTTGTTTTGGCCCATTAGCTGACTTTT
1223738 CTGAAATTTTTAAATATTTTTCCTATAAACTATATGAAATTCCCTTTCTAGAAAAGTATGATTTG
325 CTGAAATTTTTAAATATTTTTCCTATAAACTATATGAAATTCCCTTTCTAGAAAAGTATGATTTG
* *
1223803 AGATTTAATGACTCCAAATGAGTCCAGAATGATTTTTTAAATTTTACTGCACCCTCTCCCTTGTA
390 AGATTTAATGATTCCAAATGAGTTCAGAATGATTTTTTAAATTTTACTGCACCCTCTCCCTTGTA
* *
1223868 TTGGCTGTCAGTGCCGAACCAAATTTGATTTCAAAAATTTTCTCCTAGAACAAGACTTTTTGGGA
455 TTGGCTGTTAGTGCCGAACCAAATTTGATTTCAACAATTTTCTCCTAGAACAAGACTTTTTGGGA
*
1223933 TTTTTAGAATATTTTCTTATTAATTCTCATTGAGTTACCATTCCAACAGTACCTCGTTCTCACTA
520 TTTTTAGAATATTTTCTTATTAATTCTCATTGAGTTACCATTCCAACAATACCTCGTTCTCACTA
* * *
1223998 GAAGCTTTTAGATGAGCTGAAATAATCTCGAAAAGGAAGACCGTAATTG
585 GAAGCTTTTAGATGAGCCGAAATAAACTCGAAAAGGAAGACCCTAATTG
* *
1224047 TCATAGACCCTAATTGTTAGATATTCGTGTGTCCAACACCTTGATATGTGTCTAGAGAGACCTAG
1 TCATAGACCCTAATTGTCAGATATTCGTGTGTCCAACACCTTGATATGTGTCTAGAAAGACCTAG
* * *
1224112 ACCCAAAATATCCCTTGTTTGGTATTGGTGACATTTTGACTCCAAATTGAAAAATTATTTAAGAA
66 ACCCAAAAAACCCCTTGTTTGGTATTGGTGACATTTTGACCCCAAATTGAAAAATTATTTAAGAA
* * *
1224177 CTCTAGACGATTTTTATAGAATTTTATAATATTTTCTCTCAAAGGATTTCGAATTATCTATCTAA
131 CTCTAGACGATTTTTATGGAATTTTATGATATTTTCTCTCAAAGG-TATCGAATTATCTATCTAA
*
1224242 TGGTATCACATTTGCCCTTAGATGTGCTCAGATGAGAGAGTTATAATTTTTCAAACTTTCATTAT
195 TGGTATCTCATTTGCCCTTAGATGTGCTCAGATGAGAGAGTTATAATTTTTCAAACTTTCATTAT
1224307 CTGGTACCCTTGGAATTAGCAATTAACATTTTATTTGGGTTGTTTTGGCCCATTAGCTGACTTTT
260 CTGGTACCCTTGGAATTAGCAATTAACATTTTATTTGGGTTGTTTTGGCCCATTAGCTGACTTTT
* *
1224372 TTGAAATTTTTAAATATTTTTCCTATAAACTATATGAAATTCCCTTTCTAGAAAAGTGTGATTTG
325 CTGAAATTTTTAAATATTTTTCCTATAAACTATATGAAATTCCCTTTCTAGAAAAGTATGATTTG
* * * * *
1224437 AGATTTAATGATTCCAAATGAGTTCAGAATAATTTTTTAAAATTTGCTGCACCCTTTCCCTTATA
390 AGATTTAATGATTCCAAATGAGTTCAGAATGATTTTTTAAATTTTACTGCACCCTCTCCCTTGTA
* * *
1224502 TTGGTTGTTAGTGCCGAACCAAATTTGATTTCAACAATTTTCTCCTAGAACAAGATTTTTTGGAA
455 TTGGCTGTTAGTGCCGAACCAAATTTGATTTCAACAATTTTCTCCTAGAACAAGACTTTTTGGGA
* *
1224567 TTTTAAAAATATTTTCTTATTAATTCTCATTGAGTTACCATTCCAACAATACCTCGTTCTCACTA
520 TTTTTAGAATATTTTCTTATTAATTCTCATTGAGTTACCATTCCAACAATACCTCGTTCTCACTA
*
1224632 GAAGCTTTTAGATGAGCCGAAATAAACTCAAAAAGGAAGA
585 GAAGCTTTTAGATGAGCCGAAATAAACTCGAAAAGGAAGA
1224672 TAGCGTAATG
Statistics
Matches: 1195, Mismatches: 61, Indels: 5
0.95 0.05 0.00
Matches are distributed among these distances:
633 56 0.05
634 1139 0.95
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (633 bp):
TCATAGACCCTAATTGTCAGATATTCGTGTGTCCAACACCTTGATATGTGTCTAGAAAGACCTAG
ACCCAAAAAACCCCTTGTTTGGTATTGGTGACATTTTGACCCCAAATTGAAAAATTATTTAAGAA
CTCTAGACGATTTTTATGGAATTTTATGATATTTTCTCTCAAAGGTATCGAATTATCTATCTAAT
GGTATCTCATTTGCCCTTAGATGTGCTCAGATGAGAGAGTTATAATTTTTCAAACTTTCATTATC
TGGTACCCTTGGAATTAGCAATTAACATTTTATTTGGGTTGTTTTGGCCCATTAGCTGACTTTTC
TGAAATTTTTAAATATTTTTCCTATAAACTATATGAAATTCCCTTTCTAGAAAAGTATGATTTGA
GATTTAATGATTCCAAATGAGTTCAGAATGATTTTTTAAATTTTACTGCACCCTCTCCCTTGTAT
TGGCTGTTAGTGCCGAACCAAATTTGATTTCAACAATTTTCTCCTAGAACAAGACTTTTTGGGAT
TTTTAGAATATTTTCTTATTAATTCTCATTGAGTTACCATTCCAACAATACCTCGTTCTCACTAG
AAGCTTTTAGATGAGCCGAAATAAACTCGAAAAGGAAGACCCTAATTG
Found at i:1230261 original size:20 final size:21
Alignment explanation
Indices: 1230228--1230267 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1230218 AAAGGTCAAA
1230228 ACCCTAGAAATATCGATACAG
1 ACCCTAGAAATATCGATACAG
*
1230249 ACCC-AGAAGTATCGATACA
1 ACCCTAGAAATATCGATACA
1230268 TATTGCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (21 bp):
ACCCTAGAAATATCGATACAG
Found at i:1230836 original size:23 final size:23
Alignment explanation
Indices: 1230809--1230853 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1230799 AACCTTGGGT
1230809 TATAATCTCTT-AAGAATTTGAGG
1 TATAAT-TCTTGAAGAATTTGAGG
*
1230832 TATAATTCTTGAAGAGTTTGAG
1 TATAATTCTTGAAGAATTTGAG
1230854 AGGTTCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (23 bp):
TATAATTCTTGAAGAATTTGAGG
Found at i:1238561 original size:34 final size:36
Alignment explanation
Indices: 1238517--1238584 Score: 86
Period size: 34 Copynumber: 1.9 Consensus size: 36
1238507 TTTCTTTATC
* * *
1238517 CTCAAGGAGCAGGACG-TACT-CATTTTCCTTTGTT
1 CTCAAAGAGCAAGACGCTACTCCATTTCCCTTTGTT
1238551 CTCAAAGAGCAAGACGCTTACTCCATTTCCCTTT
1 CTCAAAGAGCAAGACGC-TACTCCATTTCCCTTT
1238585 ATCCTTGAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 14 0.50
36 4 0.14
37 10 0.36
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (36 bp):
CTCAAAGAGCAAGACGCTACTCCATTTCCCTTTGTT
Found at i:1238768 original size:77 final size:78
Alignment explanation
Indices: 1238659--1238806 Score: 174
Period size: 80 Copynumber: 1.9 Consensus size: 78
1238649 TTTCATCTTC
* *
1238659 TTTTCCCTTTGTCCTAAAAAAGTAGGACGCA-TTTCATTTCCTTCTTCCTTTGTCCTCGAA-GAG
1 TTTTCCCTTTATCCTAAAAAAGCAGGACGCATTTTCATTTCCTTCTTCCTTTGTCCTC-AAGGAG
1238722 CAAGATGTATCTCA
65 CAAGATGTATCTCA
* ** * ** *
1238736 TTTTCCCTTTATCCTCAAGGAGCAGGATGCATTCTTTTTTTTCCTTTTTCCTTTGTCCTCAAGGA
1 TTTTCCCTTTATCCTAAAAAAGCAGGACGCA-T-TTTCATTTCCTTCTTCCTTTGTCCTCAAGGA
1238801 GCAAGA
64 GCAAGA
1238807 CCTATTTCAC
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
77 25 0.43
79 2 0.03
80 31 0.53
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (78 bp):
TTTTCCCTTTATCCTAAAAAAGCAGGACGCATTTTCATTTCCTTCTTCCTTTGTCCTCAAGGAGC
AAGATGTATCTCA
Found at i:1238783 original size:121 final size:120
Alignment explanation
Indices: 1238658--1238883 Score: 269
Period size: 121 Copynumber: 1.9 Consensus size: 120
1238648 ATTTCATCTT
* * * *
1238658 CTTTTCCCTTTGTCCTAAAAAAGTAGGACGC-ATTTCA-T-TTCCTTCTTCCTTTGTCCTCGAAG
1 CTTTTCCCTTTGTCCTAAAAAAGCAAGAC-CTATTTCACTATT-ATTCTTCCTTTGTCCTCAAAG
* *
1238720 AGCAAGATGTATCTCATTTTCCCTTTATCCTCAAGGAGCAGGATGCATTCTTTTTTTTC
64 AGCAAGATGTA-CTCACTTT-CCTTTATCCTCAAAGAGCAGGATGCATTCTTTTTTTTC
* * ** *
1238779 CTTTTTCCTTTGTCCTCAAGGAGCAAGACCTATTTCACTATTATTTTTCCTTTGTCCTCAAAGAG
1 CTTTTCCCTTTGTCCTAAAAAAGCAAGACCTATTTCACTATTATTCTTCCTTTGTCCTCAAAGAG
* * *
1238844 TAGGATGTACTCCCTTTCCTTTATCCTCAAAGAGCAGGAT
66 CAAGATGTACTCACTTTCCTTTATCCTCAAAGAGCAGGAT
1238884 ACCCACTCTT
Statistics
Matches: 88, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
120 23 0.26
121 35 0.40
122 28 0.32
123 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (120 bp):
CTTTTCCCTTTGTCCTAAAAAAGCAAGACCTATTTCACTATTATTCTTCCTTTGTCCTCAAAGAG
CAAGATGTACTCACTTTCCTTTATCCTCAAAGAGCAGGATGCATTCTTTTTTTTC
Found at i:1238812 original size:162 final size:163
Alignment explanation
Indices: 1238541--1238848 Score: 419
Period size: 162 Copynumber: 1.9 Consensus size: 163
1238531 CGTACTCATT
* ** *
1238541 TTCCTTTGTTCTCAAAGAGCAAGACGCTTACTCCATTTCCCTTTATCCTTGAGGAGTAGGATGCA
1 TTCCTTTGTCCTCAAAGAGCAAGACGCTTACTCCATTTCCCTTTATCCTCAAGGAGCAGGATGCA
* * * *
1238606 TTCCTTTTTTTCCTTTTTCTTTGTCTTCAAGGAGTAGAACCTATTTCA-TCTTCTTTTCCCTTTG
66 TTCCTTTTTTTCCTTTTTCTTTGTCCTCAAGGAGAAGAACCTATTTCACTATTATTTTCCCTTTG
1238670 TCCTAAAAAAGTAGGACGCATTTCATTTCCTTC
131 TCCTAAAAAAGTAGGACGCATTTCATTTCCTTC
* *
1238703 TTCCTTTGTCCTCGAAGAGCAAGATG--TA-TCTCATTTTCCCTTTATCCTCAAGGAGCAGGATG
1 TTCCTTTGTCCTCAAAGAGCAAGACGCTTACTC-CA-TTTCCCTTTATCCTCAAGGAGCAGGATG
* *
1238765 CATTCTTTTTTTTCCTTTTTCCTTTGTCCTCAAGGAGCAAG-ACCTATTTCACTATTATTTTTCC
64 CATTCCTTTTTTTCCTTTTT-CTTTGTCCTCAAGGAG-AAGAACCTATTTCACTATTATTTTCCC
* *
1238829 TTTGTCCTCAAAGAGTAGGA
127 TTTGTCCTAAAAAAGTAGGA
1238849 TGTACTCCCT
Statistics
Matches: 127, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
159 2 0.02
160 4 0.03
161 44 0.35
162 48 0.38
163 29 0.23
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (163 bp):
TTCCTTTGTCCTCAAAGAGCAAGACGCTTACTCCATTTCCCTTTATCCTCAAGGAGCAGGATGCA
TTCCTTTTTTTCCTTTTTCTTTGTCCTCAAGGAGAAGAACCTATTTCACTATTATTTTCCCTTTG
TCCTAAAAAAGTAGGACGCATTTCATTTCCTTC
Found at i:1239014 original size:31 final size:31
Alignment explanation
Indices: 1238968--1239046 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
1238958 GAGCTAGTGG
* * *
1238968 CACCCTAGTTAAAGCCCGCAAGAGTTGACGA
1 CACCCGAGTCAAAGCCCGCAAGAGTTGACAA
* * ** *
1238999 CACCCGAGTCTAAGCCTGCGTGAGTTGGCAA
1 CACCCGAGTCAAAGCCCGCAAGAGTTGACAA
*
1239030 CACCTGAGTCAAAGCCC
1 CACCCGAGTCAAAGCCC
1239047 ACACAAGTTG
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.28, C:0.32, G:0.24, T:0.16
Consensus pattern (31 bp):
CACCCGAGTCAAAGCCCGCAAGAGTTGACAA
Found at i:1239065 original size:31 final size:31
Alignment explanation
Indices: 1239030--1239185 Score: 89
Period size: 37 Copynumber: 4.7 Consensus size: 31
1239020 GAGTTGGCAA
*
1239030 CACCTGAGTCAAAGCCCACACAAGTTGGTGG
1 CACCTAAGTCAAAGCCCACACAAGTTGGTGG
* ** * * *
1239061 CACCTAAATCTAAGTTTAAGATCGCACGAGTTGGTAG
1 CACCTAAGTC--A----AAGCCCACACAAGTTGGTGG
* *
1239098 CACCTAAGTCAAAGCCTACACAAGCTGGTGG
1 CACCTAAGTCAAAGCCCACACAAGTTGGTGG
* *
1239129 CACCTAAATCTAAGTCTAAGCTCACACAAGTTGGTGG
1 CA-C-----CTAAGTCAAAGCCCACACAAGTTGGTGG
*
1239166 CACCTGAGTCAAAG-CCACAC
1 CACCTAAGTCAAAGCCCACAC
1239186 GAGTCCCACA
Statistics
Matches: 91, Mismatches: 22, Indels: 25
0.66 0.16 0.18
Matches are distributed among these distances:
30 5 0.05
31 32 0.35
32 1 0.01
33 1 0.01
35 1 0.01
36 1 0.01
37 50 0.55
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (31 bp):
CACCTAAGTCAAAGCCCACACAAGTTGGTGG
Found at i:1239093 original size:37 final size:36
Alignment explanation
Indices: 1239048--1239170 Score: 121
Period size: 37 Copynumber: 3.5 Consensus size: 36
1239038 TCAAAGCCCA
*
1239048 CACAAGTTGGTGGCACCTAAATCTAAGTTTAAGATC
1 CACAAGTTGGTGGCACCTAAATCTAAGTCTAAGATC
* * * * *
1239084 GCACGAGTTGGTAGCACCTAAGTCAAAGCCT---A--
1 -CACAAGTTGGTGGCACCTAAATCTAAGTCTAAGATC
* *
1239116 CACAAGCTGGTGGCACCTAAATCTAAGTCTAAGCTC
1 CACAAGTTGGTGGCACCTAAATCTAAGTCTAAGATC
1239152 ACACAAGTTGGTGGCACCT
1 -CACAAGTTGGTGGCACCT
1239171 GAGTCAAAGC
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
31 24 0.36
34 1 0.02
37 41 0.62
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (36 bp):
CACAAGTTGGTGGCACCTAAATCTAAGTCTAAGATC
Found at i:1239129 original size:68 final size:67
Alignment explanation
Indices: 1239020--1239185 Score: 233
Period size: 68 Copynumber: 2.4 Consensus size: 67
1239010 AAGCCTGCGT
* * * * *
1239020 GAGTTGGCAACACCTGAGTCAAAGCCCACACAAGTTGGTGGCACCTAAATCTAAGTTTAAGATCG
1 GAGTTGGTAGCACCTGAGTCAAAG-CCACACAAGCTGGTGGCACCTAAATCTAAGTCTAAGATCA
1239085 CAC
65 CAC
* *
1239088 GAGTTGGTAGCACCTAAGTCAAAGCCTACACAAGCTGGTGGCACCTAAATCTAAGTCTAAGCTCA
1 GAGTTGGTAGCACCTGAGTCAAAGCC-ACACAAGCTGGTGGCACCTAAATCTAAGTCTAAGATCA
1239153 CAC
65 CAC
* *
1239156 AAGTTGGTGGCACCTGAGTCAAAGCCACAC
1 GAGTTGGTAGCACCTGAGTCAAAGCCACAC
1239186 GAGTCCCACA
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
67 6 0.07
68 81 0.93
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (67 bp):
GAGTTGGTAGCACCTGAGTCAAAGCCACACAAGCTGGTGGCACCTAAATCTAAGTCTAAGATCAC
AC
Found at i:1239202 original size:41 final size:41
Alignment explanation
Indices: 1239151--1239263 Score: 181
Period size: 41 Copynumber: 2.8 Consensus size: 41
1239141 AGTCTAAGCT
* *
1239151 CACACAAGTTGGTGGCACCTGAGTCAAAGCCACACGAGTCC
1 CACACAAGTTGGTGGCACCTAAGTCAAAGCCACACGAATCC
*
1239192 CACACAAGTTGGTGGCACCTAAGTCAAAGCCACACGAATCT
1 CACACAAGTTGGTGGCACCTAAGTCAAAGCCACACGAATCC
* *
1239233 CACACAAGTTGGTGGCATCTTAGTCAAAGCC
1 CACACAAGTTGGTGGCACCTAAGTCAAAGCC
1239264 TGCGCAAGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (41 bp):
CACACAAGTTGGTGGCACCTAAGTCAAAGCCACACGAATCC
Found at i:1239336 original size:31 final size:30
Alignment explanation
Indices: 1239233--1239395 Score: 101
Period size: 31 Copynumber: 5.3 Consensus size: 30
1239223 ACACGAATCT
* * *
1239233 CACACAAGTTGGTGGCATCTTAGTCAAAGC
1 CACACAAGTTGGCGGCACCTGAGTCAAAGC
* * * * * *
1239263 CTGCGCAAGCTGGTGGCACCTGGGTCTAAGC
1 C-ACACAAGTTGGCGGCACCTGAGTCAAAGC
** ** *
1239294 TTGCATGAGTTGGCAGCACCTGAGTCAAAGC
1 -CACACAAGTTGGCGGCACCTGAGTCAAAGC
* * *
1239325 ACACACAAGTTGGTGGCACCCGAGTCTAAGC
1 -CACACAAGTTGGCGGCACCTGAGTCAAAGC
** *
1239356 CAGCATGAGTTGGCGGCACTTGAGTCAAAGC
1 CA-CACAAGTTGGCGGCACCTGAGTCAAAGC
1239387 TCACACAAG
1 -CACACAAG
1239396 CTAGTGGCAC
Statistics
Matches: 96, Mismatches: 33, Indels: 7
0.71 0.24 0.05
Matches are distributed among these distances:
30 3 0.03
31 91 0.95
32 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (30 bp):
CACACAAGTTGGCGGCACCTGAGTCAAAGC
Found at i:1239339 original size:62 final size:62
Alignment explanation
Indices: 1239268--1239413 Score: 202
Period size: 62 Copynumber: 2.4 Consensus size: 62
1239258 AAAGCCTGCG
* **
1239268 CAAGCTGGTGGCACCTGGGTCTAAGCTTGCATGAGTTGGCAGCACCTGAGTCAAAGCACACA
1 CAAGCTGGTGGCACCTGAGTCTAAGCCAGCATGAGTTGGCAGCACCTGAGTCAAAGCACACA
* * * * *
1239330 CAAGTTGGTGGCACCCGAGTCTAAGCCAGCATGAGTTGGCGGCACTTGAGTCAAAGCTCACA
1 CAAGCTGGTGGCACCTGAGTCTAAGCCAGCATGAGTTGGCAGCACCTGAGTCAAAGCACACA
* *
1239392 CAAGCTAGTGGCACCTAAGTCT
1 CAAGCTGGTGGCACCTGAGTCT
1239414 GAGTCAAAGC
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (62 bp):
CAAGCTGGTGGCACCTGAGTCTAAGCCAGCATGAGTTGGCAGCACCTGAGTCAAAGCACACA
Found at i:1239434 original size:37 final size:37
Alignment explanation
Indices: 1239376--1239525 Score: 159
Period size: 37 Copynumber: 4.2 Consensus size: 37
1239366 TGGCGGCACT
*
1239376 TGAGTCAAAGCTCACACAAGCTAGTGGCACCTAAGTC
1 TGAGTCAAAGCCCACACAAGCTAGTGGCACCTAAGTC
* * ** *
1239413 TGAGTCAAAGCCCGCATAAGCT-GACG-A-C--A-CC
1 TGAGTCAAAGCCCACACAAGCTAGTGGCACCTAAGTC
*
1239444 TGAGTCAAAGCCCACACAAGCTAATGGCACCTAAGTC
1 TGAGTCAAAGCCCACACAAGCTAGTGGCACCTAAGTC
* * *
1239481 TGAGTCAAAGCTCACACAAGCTAGTGACACATAAGTC
1 TGAGTCAAAGCCCACACAAGCTAGTGGCACCTAAGTC
*
1239518 CGAGTCAA
1 TGAGTCAA
1239526 GTCCACATTA
Statistics
Matches: 90, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
31 21 0.23
32 2 0.02
33 1 0.01
34 2 0.02
35 1 0.01
36 3 0.03
37 60 0.67
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.17
Consensus pattern (37 bp):
TGAGTCAAAGCCCACACAAGCTAGTGGCACCTAAGTC
Found at i:1239450 original size:68 final size:68
Alignment explanation
Indices: 1239310--1239491 Score: 214
Period size: 68 Copynumber: 2.8 Consensus size: 68
1239300 GAGTTGGCAG
* * * * * *
1239310 CACCTGAGTCAAAGCACACACAAGTTGGTGGCACC-----C-GAGTCTAAGCCAGCATGAGTTGG
1 CACCTGAGTCAAAGCACACACAAGCTAGTGGCACCTAAGTCTGAGTCAAAGCCAGCATAAGCTGA
*
1239369 CGG
66 CGA
* * *
1239372 CACTTGAGTCAAAGCTCACACAAGCTAGTGGCACCTAAGTCTGAGTCAAAGCCCGCATAAGCTGA
1 CACCTGAGTCAAAGCACACACAAGCTAGTGGCACCTAAGTCTGAGTCAAAGCCAGCATAAGCTGA
1239437 CGA
66 CGA
* *
1239440 CACCTGAGTCAAAGCCCACACAAGCTAATGGCACCTAAGTCTGAGTCAAAGC
1 CACCTGAGTCAAAGCACACACAAGCTAGTGGCACCTAAGTCTGAGTCAAAGC
1239492 TCACACAAGC
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
62 31 0.31
67 1 0.01
68 69 0.68
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (68 bp):
CACCTGAGTCAAAGCACACACAAGCTAGTGGCACCTAAGTCTGAGTCAAAGCCAGCATAAGCTGA
CGA
Found at i:1240120 original size:20 final size:20
Alignment explanation
Indices: 1240080--1240134 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1240070 TTCTACAATT
* *
1240080 TGTATCGACACAATTAGTGAA
1 TGTATCGATAC-ATAAGTGAA
1240101 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
1240121 TGTATCGATACATA
1 TGTATCGATACATA
1240135 TTTTAAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 22 0.69
21 10 0.31
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:1240145 original size:21 final size:20
Alignment explanation
Indices: 1240080--1240150 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
1240070 TTCTACAATT
* * *
1240080 TGTATCGACACAATTAGTGAA
1 TGTATCGATAC-ATAAGTAAA
*
1240101 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTAAA
**
1240121 TGTATCGATACATATTTTAAA
1 TGTATCGATACATA-AGTAAA
1240142 TGTATCGAT
1 TGTATCGAT
1240151 CCAAGACCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 22 0.50
21 22 0.50
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATAAGTAAA
Found at i:1247282 original size:42 final size:42
Alignment explanation
Indices: 1247163--1248268 Score: 688
Period size: 42 Copynumber: 26.1 Consensus size: 42
1247153 TGCTTAGGGA
* * ** * *
1247163 TGACCTTAGAGACTTTCTTACCCTCAGTCTATCTATCAGCTT
1 TGACCCTAGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTT
* * * * *
1247205 TGA-CCTCGAAGA-TTGCCTCACC-TCAAGTGTGCCTGTCGGTTT
1 TGACCCTAG-AGACTT-TCTTACCTTC-AGTCTGCCTGTCGGCTT
* **
1247247 TGACCCTAGAGACTTTCTTACCTTCAGTCTACCTGTCAACTT
1 TGACCCTAGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTT
* * * * * * ** *
1247289 TGACCTTGGAGA-TTGCCT-CATCTCAACTCTGCCAATTGGCTT
1 TGACCCTAGAGACTTTCTTACCT-TC-AGTCTGCCTGTCGGCTT
* * * * * **
1247331 TGACCCTAAAGACTTTCCTACCTCCAGTCTACCTATCGATTT
1 TGACCCTAGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTT
** * * *
1247373 TGACCCTAGAGACTGCCTCACC-TCAAGTCTGCCTATTGGCTT
1 TGACCCTAGAGACTTTCTTACCTTC-AGTCTGCCTGTCGGCTT
* * * * *
1247415 TGACCTTGGAGACTTTCTTACCCTCAGTCTGCTTGTCAGCTT
1 TGACCCTAGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTT
* * * * * * **
1247457 TGACCCTGGAGA-TTGCCTCATCTTAAGTCTACCTGTTAGCTT
1 TGACCCTAGAGACTT-TCTTACCTTCAGTCTGCCTGTCGGCTT
* * * * *
1247499 TGA-CCTTGAAGATTTTCCTACCTTTAGTCTGCCTATCGGCTT
1 TGACCCTAG-AGACTTTCTTACCTTCAGTCTGCCTGTCGGCTT
* * * *
1247541 TGACCCTAGAGACTGTCTCATC-TCAAGTCTGCCTGTCAGCTT
1 TGACCCTAGAGACTTTCTTACCTTC-AGTCTGCCTGTCGGCTT
* * * * *
1247583 TGACCCTGGAGACTTTCTTACCCTTCAATCTGCTTATCGACTT
1 TGACCCTAGAGACTTTCTTA-CCTTCAGTCTGCCTGTCGGCTT
* * *
1247626 TGACCCTAGAGACTGTT-TAATCTTAAGTCTGCCTGTCGGCTT
1 TGACCCTAGAGACT-TTCTTACCTTCAGTCTGCCTGTCGGCTT
* * * * * *
1247668 TGACCTTGGAGACTTTTTTACCCCTCAAGTCTGCTTGTCAGCTT
1 TGACCCTAGAGACTTTCTTA-CCTTC-AGTCTGCCTGTCGGCTT
*
1247712 TGACCTTAGAGACTTT-TTCACACTTCAGTCTGCCTGTCGGCTT
1 TGACCCTAGAGACTTTCTT-AC-CTTCAGTCTGCCTGTCGGCTT
* ** * * * * **
1247755 TGACCTTAGAGACTACCTCATC-TCAAGTCTACTTGTTAGCTT
1 TGACCCTAGAGACTTTCTTACCTTC-AGTCTGCCTGTCGGCTT
* * *
1247797 TGACCTTGGAGACTTTCTTACCCTTCAGTCTGCCTG-CTAGCTT
1 TGACCCTAGAGACTTTCTTA-CCTTCAGTCTGCCTGTC-GGCTT
* * * * * * *
1247840 TAACGCTGGAGACTTTCTTACCCTCAGTTTGCCTATCGGCGT
1 TGACCCTAGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTT
* ** * * *
1247882 TGACTCTAGAGACTGCCTCATC-TCAAGTCTGCTTGTCGGCTT
1 TGACCCTAGAGACTTTCTTACCTTC-AGTCTGCCTGTCGGCTT
** * *
1247924 TGACTTTGGAGACTTTCTTACCCTTCAGTCTGCTTGTCGGCTT
1 TGACCCTAGAGACTTTCTTA-CCTTCAGTCTGCCTGTCGGCTT
* * *
1247967 TGATCCTTGAGACTTTCTTACCCTCAGTCTGCCTGTCGGCTT
1 TGACCCTAGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTT
* ** * * *
1248009 TGACCTTAGAGACTGCCTCATC-TCAAGTCTGCCTGTTGGCTT
1 TGACCCTAGAGACTTTCTTACCTTC-AGTCTGCCTGTCGGCTT
* * *
1248051 TGACCCTGGAGACTTTTTTACGC-TCAGTCTGCCTATCGGCTT
1 TGACCCTAGAGACTTTCTTAC-CTTCAGTCTGCCTGTCGGCTT
1248093 TGACCCTAGAGACTTT-TCTACC-TCAAGTCTGCCTGTCGGCTT
1 TGACCCTAGAGACTTTCT-TACCTTC-AGTCTGCCTGTCGGCTT
*
1248135 TGACCCTAGAGAC-TTCTTTATCC-TCAAGTCTGCTTGTCGGCTT
1 TGACCCTAGAGACTTTC-TTA-CCTTC-AGTCTGCCTGTCGGCTT
* * *
1248178 TGACCTTGGAGACTTTCTTA-CTCTCATGTCTGCCTATCGGCTT
1 TGACCCTAGAGACTTTCTTACCT-TCA-GTCTGCCTGTCGGCTT
* * ** * * *
1248221 TGACCTTAGAGACTTTTTTACCTTTTGTCTGTCGGTTGGCTT
1 TGACCCTAGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTT
1248263 TGACCC
1 TGACCC
1248269 AGAAGAATCC
Statistics
Matches: 820, Mismatches: 198, Indels: 92
0.74 0.18 0.08
Matches are distributed among these distances:
40 2 0.00
41 36 0.04
42 507 0.62
43 225 0.27
44 50 0.06
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.36
Consensus pattern (42 bp):
TGACCCTAGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTT
Found at i:1247680 original size:127 final size:127
Alignment explanation
Indices: 1247163--1248242 Score: 895
Period size: 127 Copynumber: 8.5 Consensus size: 127
1247153 TGCTTAGGGA
* ** * * * *
1247163 TGACCTTAGAGACTTTCTTACCCTCAGTCTATCTATCAGCTTTGA-CCTCGAAGA-TTGCCT-CA
1 TGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCAGCTTTGACCCTAG-AGACTTTCTTAC-
* * * ** * * * **
1247225 CC-TCAAGTGTGCCTGTCGGTTTTGACCCTAGAGACTTTCTTACCTTC-AGTCTACCTGTCAACT
64 CCTTC-AGTCTGCCTATCGGCTTTGACCCTAGAGACTGCCTCATC-TCAAGTCTGCCTGTCGGCT
1247288 T
127 T
* * * * ** ** * *
1247289 TGACCTTGGAGA-TTGCCT-CATCTCAACTCTGCCAATTGGCTTTGACCCTAAAGACTTTCCTA-
1 TGACCTTGGAGACTTTCTTAC-CCTC-AGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTAC
* * ** * * *
1247351 CCTCCAGTCTACCTATCGATTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTATTGGCTT
64 CCTTCAGTCTGCCTATCGGCTTTGACCCTAGAGACTGCCTCATCTCAAGTCTGCCTGTCGGCTT
* * * * *
1247415 TGACCTTGGAGACTTTCTTACCCTCAGTCTGCTTGTCAGCTTTGACCCTGGAGA-TTGCCT-CAT
1 TGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTAC-C
* * * ** * * * * ** *
1247478 CTTAAGTCTACCTGTTAGCTTTGA-CCTTGAAGATTTTCCT-ACCTTTAGTCTGCCTATCGGCTT
65 CTTCAGTCTGCCTATCGGCTTTGACCCTAG-AGA-CTGCCTCATCTCAAGTCTGCCTGTCGGCTT
* * * * * *
1247541 TGACCCTAGAGACTGTCTCA-TCTCAAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCTTACC
1 TGACCTTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACC
* * * ** * *
1247605 CTTCAATCTGCTTATCGACTTTGACCCTAGAGACTGTTTAATCTTAAGTCTGCCTGTCGGCTT
65 CTTCAGTCTGCCTATCGGCTTTGACCCTAGAGACTGCCTCATCTCAAGTCTGCCTGTCGGCTT
* * *
1247668 TGACCTTGGAGACTTTTTTACCCCTCAAGTCTGCTTGTCAGCTTTGACCTTAGAGACTTT-TTCA
1 TGACCTTGGAGACTTTCTTA-CCCTC-AGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTT-A
* * * * * * **
1247732 CACTTCAGTCTGCCTGTCGGCTTTGACCTTAGAGACTACCTCATCTCAAGTCTACTTGTTAGCTT
63 CCCTTCAGTCTGCCTATCGGCTTTGACCCTAGAGACTGCCTCATCTCAAGTCTGCCTGTCGGCTT
* * *
1247797 TGACCTTGGAGACTTTCTTACCCTTCAGTCTGCCTG-CTAGCTTTAACGCTGGAGACTTTCTTAC
1 TGACCTTGGAGACTTTCTTACCC-TCAGTCTGCCTGTC-AGCTTTGACCCTAGAGACTTTCTTAC
* * * *
1247861 CC-TCAGTTTGCCTATCGGCGTTGACTCTAGAGACTGCCTCATCTCAAGTCTGCTTGTCGGCTT
64 CCTTCAGTCTGCCTATCGGCTTTGACCCTAGAGACTGCCTCATCTCAAGTCTGCCTGTCGGCTT
* * * * *
1247924 TGACTTTGGAGACTTTCTTACCCTTCAGTCTGCTTGTCGGCTTTGATCCTTGAGACTTTCTTACC
1 TGACCTTGGAGACTTTCTTACCC-TCAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACC
* * *
1247989 C-TCAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCTCATCTCAAGTCTGCCTGTTGGCTT
65 CTTCAGTCTGCCTATCGGCTTTGACCCTAGAGACTGCCTCATCTCAAGTCTGCCTGTCGGCTT
* * * * *
1248051 TGACCCTGGAGACTTTTTTACGCTCAGTCTGCCTATCGGCTTTGACCCTAGAGACTTT-TCTA-C
1 TGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCT-TACC
* * * * *
1248114 C-TCAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTTATCCTCAAGTCTGCTTGTCGGCTT
65 CTTC-AGTCTGCCTATCGGCTTTGACCCTAGAGACTGCCTCAT-CTCAAGTCTGCCTGTCGGCTT
* * * * *
1248178 TGACCTTGGAGACTTTCTTACTCTCATGTCTGCCTATCGGCTTTGACCTTAGAGACTTTTTTACC
1 TGACCTTGGAGACTTTCTTACCCTCA-GTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACC
1248243 TTTTGTCTGT
Statistics
Matches: 774, Mismatches: 149, Indels: 59
0.79 0.15 0.06
Matches are distributed among these distances:
124 1 0.00
125 26 0.03
126 260 0.34
127 303 0.39
128 74 0.10
129 110 0.14
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.36
Consensus pattern (127 bp):
TGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACCC
TTCAGTCTGCCTATCGGCTTTGACCCTAGAGACTGCCTCATCTCAAGTCTGCCTGTCGGCTT
Found at i:1248251 original size:85 final size:84
Alignment explanation
Indices: 1247163--1248267 Score: 764
Period size: 84 Copynumber: 13.1 Consensus size: 84
1247153 TGCTTAGGGA
* ** * * * * *
1247163 TGACCTTAGAGACTTTCTTACCCTCAGTCTATCTATCAGCTTTGA-CCTCGAAGA-TTGCCTCAC
1 TGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTAG-AGACTT-TCTTAC
* * *
1247226 CTCAAGTGTGCCTGTCGGTTT
64 CTTAAGTCTGCCTGTCGGCTT
* * * * ** * * * * *
1247247 TGACCCTAGAGACTTTCTTACCTTCAGTCTACCTGTCAACTTTGACCTTGGAGA-TTGCCTCATC
1 TGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTT-TCTTACC
* * ** *
1247311 TCAACTCTGCCAATTGGCTT
65 TTAAGTCTGCCTGTCGGCTT
* ** * * * ** ** *
1247331 TGACCCTAAAGACTTTCCTA-CCTCCAGTCTACCTATCGATTTTGACCCTAGAGACTGCCTCACC
1 TGACCTTGGAGACTTTCTTACCCT-CAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACC
* * *
1247395 TCAAGTCTGCCTATTGGCTT
65 TTAAGTCTGCCTGTCGGCTT
* * * * * *
1247415 TGACCTTGGAGACTTTCTTACCCTCAGTCTGCTTGTCAGCTTTGACCCTGGAGA-TTGCCTCATC
1 TGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTT-TCTTACC
* **
1247479 TTAAGTCTACCTGTTAGCTT
65 TTAAGTCTGCCTGTCGGCTT
* * * * * * * * *
1247499 TGACCTTGAAGATTTTCCTACCTTTAGTCTGCCTATCGGCTTTGACCCTAGAGACTGTCTCATCT
1 TGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCT
* *
1247564 CAAGTCTGCCTGTCAGCTT
66 TAAGTCTGCCTGTCGGCTT
* * * * * * *
1247583 TGACCCTGGAGACTTTCTTACCCTTCAATCTGCTTATCGACTTTGACCCTAGAGACTGTT-TAAT
1 TGACCTTGGAGACTTTCTTACCC-TCAGTCTGCCTGTCGGCTTTGACCCTAGAGACT-TTCTTAC
1247647 CTTAAGTCTGCCTGTCGGCTT
64 CTTAAGTCTGCCTGTCGGCTT
* * * *
1247668 TGACCTTGGAGACTTTTTTACCCCTCAAGTCTGCTTGTCAGCTTTGACCTTAGAGACTTT-TTCA
1 TGACCTTGGAGACTTTCTTA-CCCTC-AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCTT-A
*
1247732 CACTTCAGTCTGCCTGTCGGCTT
63 C-CTTAAGTCTGCCTGTCGGCTT
* ** * * * * ** * *
1247755 TGACCTTAGAGACTACCTCA-TCTCAAGTCTACTTGTTAGCTTTGACCTTGGAGACTTTCTTACC
1 TGACCTTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTA-C
* *
1247819 CTTCAGTCTGCCTG-CTAGCTT
64 CTTAAGTCTGCCTGTC-GGCTT
* * * * * ** * *
1247840 TAACGC-TGGAGACTTTCTTACCCTCAGTTTGCCTATCGGCGTTGACTCTAGAGACTGCCTCATC
1 TGAC-CTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACC
* *
1247904 TCAAGTCTGCTTGTCGGCTT
65 TTAAGTCTGCCTGTCGGCTT
* * * *
1247924 TGACTTTGGAGACTTTCTTACCCTTCAGTCTGCTTGTCGGCTTTGATCCTTGAGACTTTCTTACC
1 TGACCTTGGAGACTTTCTTACCC-TCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACC
* *
1247989 CTCAGTCTGCCTGTCGGCTT
65 TTAAGTCTGCCTGTCGGCTT
* ** * * * * *
1248009 TGACCTTAGAGACTGCCTCA-TCTCAAGTCTGCCTGTTGGCTTTGACCCTGGAGACTTTTTTACG
1 TGACCTTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTAC-
* *
1248073 C-TCAGTCTGCCTATCGGCTT
64 CTTAAGTCTGCCTGTCGGCTT
* *
1248093 TGACCCTAGAGACTTT-TCTA-CCTCAAGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TTCTTTA
1 TGACCTTGGAGACTTTCT-TACCCTC-AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTC-TTA
* *
1248155 TCCTCAAGTCTGCTTGTCGGCTT
63 -CCTTAAGTCTGCCTGTCGGCTT
* * * *
1248178 TGACCTTGGAGACTTTCTTACTCTCATGTCTGCCTATCGGCTTTGACCTTAGAGACTTTTTTACC
1 TGACCTTGGAGACTTTCTTACCCTCA-GTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACC
** * * *
1248243 TTTTGTCTGTCGGTTGGCTT
65 TTAAGTCTGCCTGTCGGCTT
1248263 TGACC
1 TGACC
1248268 CAGAAGAATC
Statistics
Matches: 823, Mismatches: 168, Indels: 59
0.78 0.16 0.06
Matches are distributed among these distances:
83 8 0.01
84 418 0.51
85 288 0.35
86 72 0.09
87 37 0.04
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.36
Consensus pattern (84 bp):
TGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCT
TAAGTCTGCCTGTCGGCTT
Found at i:1248819 original size:11 final size:10
Alignment explanation
Indices: 1248798--1248855 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
1248788 TATTTGACAT
1248798 TAAAAATTAA
1 TAAAAATTAA
1248808 TAAAAATATAA
1 TAAAAAT-TAA
1248819 TAAAAA--AA
1 TAAAAATTAA
1248827 TTAAAAATT-A
1 -TAAAAATTAA
1248837 -AAAAATTAA
1 TAAAAATTAA
1248846 -AAATAATTAA
1 TAAA-AATTAA
1248856 ATTTTAGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
8 9 0.21
9 10 0.24
10 14 0.33
11 9 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAAATTAA
Found at i:1248858 original size:15 final size:15
Alignment explanation
Indices: 1248796--1248849 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
1248786 TTTATTTGAC
1248796 ATTAAAAATTAATAAA
1 ATTAAAAATTAA-AAA
* * *
1248812 AAT-ATAATAAAAAA
1 ATTAAAAATTAAAAA
1248826 ATTAAAAATTAAAAA
1 ATTAAAAATTAAAAA
1248841 ATTAAAAAT
1 ATTAAAAAT
1248850 AATTAAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 5 0.16
15 24 0.77
16 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTAAAAATTAAAAA
Found at i:1249053 original size:67 final size:67
Alignment explanation
Indices: 1248908--1249091 Score: 261
Period size: 67 Copynumber: 2.8 Consensus size: 67
1248898 CAAAATGTAG
* ** * * *
1248908 TGGATTTCATGCTTAATTTGCTGTCACCTAAGCTTTTTAAGTG-----TCATTGCATTGCATTGC
1 TGGATTTCATGTTTAATTTGCTACCACCTAAGCTTTCTAGGTGTCATTTCATTGCATTACATTGC
1248968 AT
66 AT
*
1248970 TGGATTTCATGTTTAATTTGCTACCACCTACGCTTTCTAGGTGTCATTTCATTGCATTACATTGC
1 TGGATTTCATGTTTAATTTGCTACCACCTAAGCTTTCTAGGTGTCATTTCATTGCATTACATTGC
1249035 AT
66 AT
*
1249037 TGGATTTCATGTTTAATTTGCTACCACCTAAGCTTTCTAGGTGTCATTACATTGC
1 TGGATTTCATGTTTAATTTGCTACCACCTAAGCTTTCTAGGTGTCATTTCATTGC
1249092 CTTGCATTTC
Statistics
Matches: 108, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
62 37 0.34
67 71 0.66
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (67 bp):
TGGATTTCATGTTTAATTTGCTACCACCTAAGCTTTCTAGGTGTCATTTCATTGCATTACATTGC
AT
Found at i:1249119 original size:12 final size:12
Alignment explanation
Indices: 1249098--1249132 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1249088 TTGCCTTGCA
*
1249098 TTTCATGCATGC
1 TTTCACGCATGC
*
1249110 TTTCACGCATAC
1 TTTCACGCATGC
1249122 TTTCACGCATG
1 TTTCACGCATG
1249133 GAATCAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.37
Consensus pattern (12 bp):
TTTCACGCATGC
Found at i:1254120 original size:1 final size:1
Alignment explanation
Indices: 1254116--1254186 Score: 70
Period size: 1 Copynumber: 71.0 Consensus size: 1
1254106 TCTTTTTTAT
* * * * * * * *
1254116 AAAAATAAAAAAACAAAAAAAAAAAACAAAAGAACAAAAAAACAAAAAAAAAACAAAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1254181 AAAAAA
1 AAAAAA
1254187 GAGAGAAAAG
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.89, C:0.07, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:1254141 original size:21 final size:20
Alignment explanation
Indices: 1254116--1254186 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
1254106 TCTTTTTTAT
*
1254116 AAAAATAAAAAAACAAAAAA
1 AAAAAAAAAAAAACAAAAAA
*
1254136 AAAAAACAAAAGAAC-AAAAA
1 AAAAAA-AAAAAAACAAAAAA
*
1254156 AACAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAACAAAAAA
1254176 AAAGAAAAAAA
1 AAA-AAAAAAA
1254187 GAGAGAAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 7 0.16
20 22 0.51
21 14 0.33
ACGTcount: A:0.89, C:0.07, G:0.03, T:0.01
Consensus pattern (20 bp):
AAAAAAAAAAAAACAAAAAA
Found at i:1254159 original size:29 final size:29
Alignment explanation
Indices: 1254116--1254186 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
1254106 TCTTTTTTAT
*
1254116 AAAAATAAAAAAACAAAAAAAAAA-AACAA
1 AAAAACAAAAAAACAAAAAAAAAACAA-AA
*
1254145 AAGAACAAAAAAACAAAAAAAAAACAAAA
1 AAAAACAAAAAAACAAAAAAAAAACAAAA
*
1254174 AAAAAGAAAAAAA
1 AAAAACAAAAAAA
1254187 GAGAGAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.89, C:0.07, G:0.03, T:0.01
Consensus pattern (29 bp):
AAAAACAAAAAAACAAAAAAAAAACAAAA
Found at i:1254183 original size:8 final size:8
Alignment explanation
Indices: 1254116--1254200 Score: 59
Period size: 8 Copynumber: 10.2 Consensus size: 8
1254106 TCTTTTTTAT
*
1254116 AAAAATAA
1 AAAAAGAA
*
1254124 AAAAACAAA
1 AAAAA-GAA
*
1254133 AAAAAAAA
1 AAAAAGAA
1254141 ACAAAAGAA
1 A-AAAAGAA
1254150 CAAAAA-AA
1 -AAAAAGAA
1254158 CAAAAA-AA
1 -AAAAAGAA
1254166 AAACAA-AA
1 AAA-AAGAA
1254174 AAAAAGAA
1 AAAAAGAA
1254182 AAAAAGAGA
1 AAAAAGA-A
*
1254191 GAAAAGAA
1 AAAAAGAA
1254199 AA
1 AA
1254201 GAACCTGCGT
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
7 5 0.07
8 37 0.55
9 24 0.36
10 1 0.01
ACGTcount: A:0.86, C:0.06, G:0.07, T:0.01
Consensus pattern (8 bp):
AAAAAGAA
Found at i:1254195 original size:10 final size:10
Alignment explanation
Indices: 1254116--1254203 Score: 70
Period size: 10 Copynumber: 8.2 Consensus size: 10
1254106 TCTTTTTTAT
1254116 AAAAATAAAA-
1 AAAAA-AAAAG
*
1254126 AAACAAAAAAA
1 AAA-AAAAAAG
1254137 AAAAACAAAAG
1 AAAAA-AAAAG
*
1254148 AACAAAAAAACA
1 AA-AAAAAAA-G
*
1254160 AAAAAAAAAC
1 AAAAAAAAAG
1254170 AAAAAAAAAG
1 AAAAAAAAAG
1254180 AAAAAAAGAGAG
1 AAAAAAA-A-AG
*
1254192 AAAAGAAAAG
1 AAAAAAAAAG
1254202 AA
1 AA
1254204 CCTGCGTAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
10 29 0.44
11 24 0.36
12 13 0.20
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.01
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:1254195 original size:22 final size:20
Alignment explanation
Indices: 1254116--1254188 Score: 96
Period size: 19 Copynumber: 3.6 Consensus size: 20
1254106 TCTTTTTTAT
*
1254116 AAAAATAAAAA-AACAAAAA
1 AAAAAAAAAAAGAACAAAAA
1254135 AAAAAAACAAAAGAACAAAAA
1 AAAAAAA-AAAAGAACAAAAA
*
1254156 AACAAAAAAAA-AACAAAAA
1 AAAAAAAAAAAGAACAAAAA
1254175 AAAAGAAAAAAAGA
1 AAAA-AAAAAAAGA
1254189 GAGAAAAGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
19 17 0.36
20 15 0.32
21 15 0.32
ACGTcount: A:0.88, C:0.07, G:0.04, T:0.01
Consensus pattern (20 bp):
AAAAAAAAAAAGAACAAAAA
Found at i:1255341 original size:62 final size:63
Alignment explanation
Indices: 1255270--1255737 Score: 587
Period size: 62 Copynumber: 7.6 Consensus size: 63
1255260 CCTTTCACCC
* * * * *
1255270 TTTAGTCCTCAATGAGTAGGACGCCATTTCCTTTT-GAAGCCCACACAAGTTGGTGGCACCTT
1 TTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * *
1255332 TTTAGTCCTCAAAGAGTAGGGCACCTTTTTCTTTTCAAAG-CCACACAAGTTGGTGGCACC-T
1 TTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * *
1255393 TTTAGTCCTTAAAGAGTAGGACACCTTTTCC-TTTCGAAGCCCACACAAGTTGGTGGCACCCT
1 TTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * ** * *
1255455 TCTAGTCCTCAAAGAGCAGGACACTTTTTTCTTTTCAAAGCCCACACAAGCCGGTGGTACC-C
1 TTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
** *
1255517 TTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAGGTTGGTGGCA-CTT
1 TTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * **
1255578 TTCTAGTCCTCAAAGAGCAAGACACCTTTTTCTTTTCAAAGCCCATATGAGTTGGTGGCA-CTT
1 TT-TAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* *
1255641 TTTAGTCCTCAAAGAGCAGGACGCCTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCA-CTT
1 TTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
*
1255702 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTC
1 TTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTC
1255738 TCCTTTGCCC
Statistics
Matches: 356, Mismatches: 42, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
60 8 0.02
61 129 0.36
62 167 0.47
63 52 0.15
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (63 bp):
TTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
Found at i:1255437 original size:61 final size:61
Alignment explanation
Indices: 1255265--1255735 Score: 557
Period size: 61 Copynumber: 7.6 Consensus size: 61
1255255 TCTCTCCTTT
* * * * * **
1255265 CACCCTTTAGTCCTCAATGAGTAGGACGCCATTTCCTTTTGAAGCCCACACAAGTTGGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGG
* * *
1255326 CACCTTTTTAGTCCTCAAAGAGTAGGGCACCTTTTTCTTTTCAAAG-CCACACAAGTTGGTGG
1 CACC-TTTTAGTCCTCAAAGAGCAGGACACC-TTTTCCTTTCAAAGCCCACACAAGTTGGTGG
* * *
1255388 CACCTTTTAGTCCTTAAAGAGTAGGACACCTTTTCCTTTCGAAGCCCACACAAGTTGGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGG
* * * **
1255449 CACCCTTCTAGTCCTCAAAGAGCAGGACACTTTTTTCTTTTCAAAGCCCACACAAGCCGGTGG
1 CA-CCTTTTAGTCCTCAAAGAGCAGGACAC-CTTTTCCTTTCAAAGCCCACACAAGTTGGTGG
* * ** * *
1255512 TACCCTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAGGTTGGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGG
* * * * **
1255573 CACTTTTCTAGTCCTCAAAGAGCAAGACACCTTTTTCTTTTCAAAGCCCATATGAGTTGGTGG
1 CACCTTT-TAGTCCTCAAAGAGCAGGACACC-TTTTCCTTTCAAAGCCCACACAAGTTGGTGG
* * * *
1255636 CACTTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGG
* *
1255697 CACTTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
1 CACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTT
1255736 TCTCCTTTGC
Statistics
Matches: 355, Mismatches: 48, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
60 12 0.03
61 143 0.40
62 130 0.37
63 70 0.20
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (61 bp):
CACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGG
Found at i:1255946 original size:46 final size:45
Alignment explanation
Indices: 1255884--1256078 Score: 136
Period size: 45 Copynumber: 4.4 Consensus size: 45
1255874 TTCCCCCTTA
* *
1255884 TCCTTAAAGAGTAGGACACA-TTCCATTCCCTTATTTTCCCCTTTTG
1 TCCTCAAAGAGCAGGACACACTT-CATTCCCTTATTTT-CCCTTTTG
* * * *
1255930 TCCTCAAAGAGCAGGACGCACTTTATTTCCTTCTTTTCCCTTTTG
1 TCCTCAAAGAGCAGGACACACTTCATTCCCTTATTTTCCCTTTTG
* * * * *
1255975 TCCTCAAAGAACACGACGCACTTTATTTTCC-T-TTTT--CTTTTG
1 TCCTCAAAGAGCAGGACACACTTCA-TTCCCTTATTTTCCCTTTTG
* * * * *
1256017 TCTTCAAAGAGCAGGACGCATTTCGTTTCCCTT-TTTTTCC-TTTG
1 TCCTCAAAGAGCAGGACACACTTC-ATTCCCTTATTTTCCCTTTTG
*
1256061 TCCTTGAAA-AGCAGGACA
1 TCC-TCAAAGAGCAGGACA
1256079 TACTCTTTTT
Statistics
Matches: 124, Mismatches: 18, Indels: 16
0.78 0.11 0.10
Matches are distributed among these distances:
42 29 0.23
43 5 0.04
44 18 0.15
45 37 0.30
46 33 0.27
47 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (45 bp):
TCCTCAAAGAGCAGGACACACTTCATTCCCTTATTTTCCCTTTTG
Found at i:1255984 original size:45 final size:44
Alignment explanation
Indices: 1255912--1256077 Score: 173
Period size: 45 Copynumber: 3.8 Consensus size: 44
1255902 CATTCCATTC
1255912 CCTTATTTTCCCCTTTTGTCCTCAAAGAGCAGGACGCACTTTATTT
1 CCTT-TTTT-CCCTTTTGTCCTCAAAGAGCAGGACGCACTTTATTT
* *
1255958 CCTTCTTTTCCCTTTTGTCCTCAAAGAACACGACGCACTTTATTTT
1 CCTT-TTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTTA-TTT
* *
1256004 CC-TTTTT--CTTTTGTCTTCAAAGAGCAGGACGCA-TTTCGTTT
1 CCTTTTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTT-ATTT
* *
1256045 CCCTTTTTTTCC-TTTGTCCTTGAAA-AGCAGGAC
1 -CCTTTTTTCCCTTTTGTCC-TCAAAGAGCAGGAC
1256078 ATACTCTTTT
Statistics
Matches: 104, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
41 6 0.06
42 25 0.24
43 5 0.05
44 18 0.17
45 37 0.36
46 13 0.12
ACGTcount: A:0.19, C:0.27, G:0.13, T:0.41
Consensus pattern (44 bp):
CCTTTTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTTATTT
Done.