Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold44
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: 3265628
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.28
Warning! 491382 characters in sequence are not A, C, G, or T
File 17 of 17
Found at i:3154305 original size:13 final size:14
Alignment explanation
Indices: 3154268--3154310 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 14
3154258 GCCAGTTTCT
3154268 TGTATCGATACAATG
1 TGTATCGATACAA-G
3154283 TGCATATCGATACAA-
1 TG--TATCGATACAAG
3154298 TGTATCGATACAA
1 TGTATCGATACAA
3154311 AGCATAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.42
15 4 0.15
17 11 0.42
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (14 bp):
TGTATCGATACAAG
Found at i:3161235 original size:3 final size:3
Alignment explanation
Indices: 3161227--3161254 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3161217 TCCGAGTCAC
3161227 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
3161255 TTCTTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:3162825 original size:13 final size:13
Alignment explanation
Indices: 3162807--3162834 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3162797 CCGTTACAAG
3162807 CAATGTATCGATA
1 CAATGTATCGATA
3162820 CAATGTATCGATA
1 CAATGTATCGATA
3162833 CA
1 CA
3162835 TTGTCCCATG
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:3162910 original size:20 final size:20
Alignment explanation
Indices: 3162883--3162943 Score: 90
Period size: 19 Copynumber: 3.1 Consensus size: 20
3162873 ACTGCGAGTT
3162883 TCATGTATCGATACAAT-TA
1 TCATGTATCGATACAATGTA
3162902 TCTATGTATCGATACAATGT-
1 TC-ATGTATCGATACAATGTA
*
3162922 GCATGTATCGATACAATGTA
1 TCATGTATCGATACAATGTA
3162942 TC
1 TC
3162944 GATACAAAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 19 0.51
20 17 0.46
21 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (20 bp):
TCATGTATCGATACAATGTA
Found at i:3162940 original size:13 final size:13
Alignment explanation
Indices: 3162924--3162950 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3162914 TACAATGTGC
3162924 ATGTATCGATACA
1 ATGTATCGATACA
3162937 ATGTATCGATACA
1 ATGTATCGATACA
3162950 A
1 A
3162951 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3165708 original size:21 final size:21
Alignment explanation
Indices: 3165668--3165708 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3165658 TTAAGTATAA
*
3165668 ATATTTTTCAAGCTATAAATC
1 ATATTTTTCAAGCTAAAAATC
3165689 ATATGTTTTCAAG-TAAAAAT
1 ATAT-TTTTCAAGCTAAAAAT
3165709 AATCCAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (21 bp):
ATATTTTTCAAGCTAAAAATC
Found at i:3165850 original size:19 final size:20
Alignment explanation
Indices: 3165807--3165857 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
3165797 CAAACCCAGA
* *
3165807 TGTATTGATACATATTGCTT
1 TGTATCGATACATATTGCAT
*
3165827 TGTATCGATACATGTT-CAT
1 TGTATCGATACATATTGCAT
*
3165846 TGTATCCATACA
1 TGTATCGATACA
3165858 CACTAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATATTGCAT
Found at i:3165963 original size:19 final size:19
Alignment explanation
Indices: 3165921--3165970 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
3165911 CCATACATTT
*
3165921 TATCGATACATGAAGGATTG
1 TATCGATACATG-AGGAATG
3165941 TATCGATACATG-GTGAATG
1 TATCGATACATGAG-GAATG
3165960 TATCGATACAT
1 TATCGATACAT
3165971 TGAGCCCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 1 0.04
19 15 0.54
20 12 0.43
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (19 bp):
TATCGATACATGAGGAATG
Found at i:3170650 original size:20 final size:20
Alignment explanation
Indices: 3170611--3170650 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3170601 AGTCACTTCT
*
3170611 AGGTCACAACGGGCACACCC
1 AGGTCACAACGGCCACACCC
3170631 AGGTCACAACCGGCCA-ACCC
1 AGGTCACAA-CGGCCACACCC
3170651 CCACATCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.30, C:0.42, G:0.23, T:0.05
Consensus pattern (20 bp):
AGGTCACAACGGCCACACCC
Found at i:3172827 original size:20 final size:19
Alignment explanation
Indices: 3172804--3172854 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
3172794 CATACCCAGA
*
3172804 TGTATTGATACATATTACTT
1 TGTATTGATACATATT-CAT
*
3172824 TGTATCGATACATATTCAT
1 TGTATTGATACATATTCAT
3172843 TGTATTGATACA
1 TGTATTGATACA
3172855 CACTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (19 bp):
TGTATTGATACATATTCAT
Found at i:3172961 original size:33 final size:32
Alignment explanation
Indices: 3172903--3172966 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
3172893 AAACTCACAT
3172903 TGTATCGATACATAAGGATTGTATCGATACAA
1 TGTATCGATACATAAGGATTGTATCGATACAA
* *
3172935 TGTATTGATACATGAATGATTGTATCGATACA
1 TGTATCGATACAT-AAGGATTGTATCGATACA
3172967 TGGTGAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGGATTGTATCGATACAA
Found at i:3172964 original size:20 final size:18
Alignment explanation
Indices: 3172901--3172987 Score: 58
Period size: 20 Copynumber: 4.8 Consensus size: 18
3172891 TAAAACTCAC
*
3172901 ATTGTATCGATACATAAGG
1 ATTGTATCGATACAT-ATG
3172920 ATTGTATCGATAC--A--
1 ATTGTATCGATACATATG
*
3172934 A-TGTATTGATACATGAATG
1 ATTGTATCGATACAT--ATG
*
3172953 ATTGTATCGATACATGGTG
1 ATTGTATCGATACAT-ATG
*
3172972 AAATGTATCGATACAT
1 -ATTGTATCGATACAT
3172988 TGAGCCCAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
13 10 0.18
14 1 0.02
16 1 0.02
17 1 0.02
19 16 0.29
20 26 0.47
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (18 bp):
ATTGTATCGATACATATG
Found at i:3181127 original size:20 final size:20
Alignment explanation
Indices: 3181102--3181148 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3181092 TTTTCACAAT
3181102 TTGTATCGATACATTCTTCA
1 TTGTATCGATACATTCTTCA
*
3181122 TTGTATCGATACCTTCTTCA
1 TTGTATCGATACATTCTTCA
3181142 TTGTATC
1 TTGTATC
3181149 TGTAGCAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (20 bp):
TTGTATCGATACATTCTTCA
Found at i:3182183 original size:79 final size:79
Alignment explanation
Indices: 3182096--3182263 Score: 203
Period size: 79 Copynumber: 2.1 Consensus size: 79
3182086 AAAACAGGGC
* *
3182096 TGGAGTATCCCC-TCAGATATAATGGGGTTAAAGCATCCCCGATTATGAAAAATCGATGTTTTAG
1 TGGAGTATCCCCTTCA-AAATAATGGGGTTAAAGCATCACCGATTATGAAAAATCGATGTTTTAG
* *
3182160 AAATAAAATTGTGGT
65 AAATAAAATCGGGGT
* ** * * * * * *
3182175 TGTAGTATCCCCTTCAAAATAATGGGGTTGGAGTATCACCGATTGTGGAAAATTGTTGTTTTGGA
1 TGGAGTATCCCCTTCAAAATAATGGGGTTAAAGCATCACCGATTATGAAAAATCGATGTTTTAGA
3182240 AATAAAATCGGGGT
66 AATAAAATCGGGGT
3182254 TGGAGTATCC
1 TGGAGTATCC
3182264 TCTAGTGTGG
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
79 71 0.96
80 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (79 bp):
TGGAGTATCCCCTTCAAAATAATGGGGTTAAAGCATCACCGATTATGAAAAATCGATGTTTTAGA
AATAAAATCGGGGT
Found at i:3182317 original size:51 final size:51
Alignment explanation
Indices: 3182197--3182317 Score: 181
Period size: 51 Copynumber: 2.4 Consensus size: 51
3182187 TTCAAAATAA
* * **
3182197 TGGGGTTGGAGTATCAC-CGATTGTGGAAAATTGTTGTTTTGGAAATAAAAT
1 TGGGGTTGGAGTATC-CTCTAGTGTGGAAAATTAATGTTTTGGAAATAAAAT
*
3182248 CGGGGTTGGAGTATCCTCTAGTGTGGAAAATTAATGTTTTGGAAATAAAAT
1 TGGGGTTGGAGTATCCTCTAGTGTGGAAAATTAATGTTTTGGAAATAAAAT
3182299 TGGGGTTGGAGTATCCTCT
1 TGGGGTTGGAGTATCCTCT
3182318 CGGAAATAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 1 0.02
51 62 0.98
ACGTcount: A:0.27, C:0.08, G:0.30, T:0.35
Consensus pattern (51 bp):
TGGGGTTGGAGTATCCTCTAGTGTGGAAAATTAATGTTTTGGAAATAAAAT
Found at i:3182334 original size:79 final size:77
Alignment explanation
Indices: 3182251--3182499 Score: 277
Period size: 79 Copynumber: 3.2 Consensus size: 77
3182241 ATAAAATCGG
* *
3182251 GGTTGGAGTATCCTCTAGTGTGGAAAATTAATGTTTTGGAAATAAAATTGGGGTTGGAGTATCCT
1 GGTTGGAGTATCCTCGA-TGTGGAAAATTGATGTTTTGGAAATAAAATTGGGGTTGGAGTATCC-
*
3182316 CTCGGAAATAACGA
64 CTTGGAAATAACGA
* * **
3182330 GGTTGGAGTATCCTCGATGGTGGAAAATTGATATTTTAGAAATAAAATCAGGGTTGGAGTATCCC
1 GGTTGGAGTATCCTCGAT-GTGGAAAATTGATGTTTTGGAAATAAAATTGGGGTTGGAGTATCCC
*
3182395 TTGGAAATAATGA
65 TTGGAAATAACGA
* * * * * * *
3182408 GATTGAAGTATTCC-CGATTGTTGAAAATCGATGTTTTGGATATAAAACTGAGGTTGG-GATATC
1 GGTTGGAGTA-TCCTCGA-TGTGGAAAATTGATGTTTTGGAAATAAAATTGGGGTTGGAG-TAT-
*
3182471 CCCTTGAAAATAACGA
62 CCCTTGGAAATAACGA
3182487 GGTTGGAGTATCC
1 GGTTGGAGTATCC
3182500 CCTTACAAAT
Statistics
Matches: 142, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
77 1 0.01
78 59 0.42
79 82 0.58
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (77 bp):
GGTTGGAGTATCCTCGATGTGGAAAATTGATGTTTTGGAAATAAAATTGGGGTTGGAGTATCCCT
TGGAAATAACGA
Found at i:3182353 original size:130 final size:130
Alignment explanation
Indices: 3182151--3182393 Score: 346
Period size: 130 Copynumber: 1.9 Consensus size: 130
3182141 TGAAAAATCG
* * * *
3182151 ATGTTTTAGAAATAAAATTGTGGTTGTAGTATCCCCTTCAAAATAATGGGGTTGGAGTATCACCG
1 ATGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCCTTCAAAATAACGAGGTTGGAGTATCACCG
* * * * *
3182216 ATTGTGGAAAATTGTTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCTCTAGTGTGGAAAATTA
66 ATGGTGGAAAATTGATATTTTAGAAATAAAATCAGGGTTGGAGTATCCTCTAGTGTGGAAAATTA
* * *
3182281 ATGTTTTGGAAATAAAATTGGGGTTGGAGTATCCTC-TCGGAAATAACGAGGTTGGAGTATC-CT
1 ATGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCCTTC-AAAATAACGAGGTTGGAGTATCAC-
3182344 CGATGGTGGAAAATTGATATTTTAGAAATAAAATCAGGGTTGGAGTATCC
64 CGATGGTGGAAAATTGATATTTTAGAAATAAAATCAGGGTTGGAGTATCC
3182394 CTTGGAAATA
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
129 3 0.03
130 96 0.97
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.33
Consensus pattern (130 bp):
ATGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCCTTCAAAATAACGAGGTTGGAGTATCACCG
ATGGTGGAAAATTGATATTTTAGAAATAAAATCAGGGTTGGAGTATCCTCTAGTGTGGAAAATTA
Found at i:3182521 original size:28 final size:28
Alignment explanation
Indices: 3182457--3182527 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 28
3182447 ATATAAAACT
3182457 GAGGTTGG-GATATCCCCTTGAAAATAAC
1 GAGGTTGGAG-TATCCCCTTGAAAATAAC
3182485 GAGGTTGGAGTATCCCCTT-ACAAATAAC
1 GAGGTTGGAGTATCCCCTTGA-AAATAAC
* *
3182513 GGGGTTGGAGCATCC
1 GAGGTTGGAGTATCC
3182528 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 1 0.03
28 37 0.95
29 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (28 bp):
GAGGTTGGAGTATCCCCTTGAAAATAAC
Found at i:3182521 original size:185 final size:186
Alignment explanation
Indices: 3182302--3182687 Score: 451
Period size: 186 Copynumber: 2.1 Consensus size: 186
3182292 ATAAAATTGG
* ** * * *
3182302 GGTTGGAGTATCCTCTCGGAAATAACGAGGTTGGAGTATCCTCGATGGTGGAAAATTGATATTTT
1 GGTTGGAGTATCCCCTCACAAATAACGAGGTTGGAGCATCCTCGATGGTGAAAAATCGATATTTT
* * * *
3182367 -AGAAATAAAATCAGGGTTGGAGTATC-CCTTGGAAATAATGAGATT-GAAGTATTCC-CGATTG
66 CA-AAATAAAATCAGGGTTGGAATATCTCATCGGAAATAACGAGATTAG-AGTA-TCCTCGA-TG
* * **
3182428 TTG-AAAATCGATGTTTTGGATATAAAACTGAGGTTGG-GATATCCCCTTGAAAATAACGA
127 GTGAAAAATCGATGTTTTGGAAATAAAACTGAGGTTGGAG-TATCCCCTAAAAAATAACGA
* * * *
3182487 GGTTGGAGTATCCCCTTACAAATAACGGGGTTGGAGCATCCTCGATTGTGAAAAATCGATGTTTT
1 GGTTGGAGTATCCCCTCACAAATAACGAGGTTGGAGCATCCTCGATGGTGAAAAATCGATATTTT
** * *
3182552 CAAAATAAAATGGGGGTTGGAATATCTCATCGGAAATAACGGGGTTAGAGTATCCTCGATGGTGA
66 CAAAATAAAATCAGGGTTGGAATATCTCATCGGAAATAACGAGATTAGAGTATCCTCGATGGTGA
* * *
3182617 AAAATCGATGTTTTGGAAATAAAATTGGGGTTGGAGTATCCCCTAAAAAATAACGG
131 AAAATCGATGTTTTGGAAATAAAACTGAGGTTGGAGTATCCCCTAAAAAATAACGA
*
3182673 GGTTGGAGTACCCCC
1 GGTTGGAGTATCCCC
3182688 GATTGTGGAA
Statistics
Matches: 169, Mismatches: 26, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
185 83 0.49
186 84 0.50
187 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (186 bp):
GGTTGGAGTATCCCCTCACAAATAACGAGGTTGGAGCATCCTCGATGGTGAAAAATCGATATTTT
CAAAATAAAATCAGGGTTGGAATATCTCATCGGAAATAACGAGATTAGAGTATCCTCGATGGTGA
AAAATCGATGTTTTGGAAATAAAACTGAGGTTGGAGTATCCCCTAAAAAATAACGA
Found at i:3182593 original size:79 final size:79
Alignment explanation
Indices: 3182487--3182798 Score: 356
Period size: 79 Copynumber: 3.9 Consensus size: 79
3182477 AAAATAACGA
* * * * * *
3182487 GGTTGGAGTATCCCCTTACAAATAACGGGGTTGGAGCATCCTCGATTGTGAAAAATCGATGTTTT
1 GGTTGGAGTATCTCCTAAGAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTT
* *
3182552 CAAAATAAAATGGG
66 GAAAATAAAATCGG
* * ** * *
3182566 GGTTGGAATATCTCATCGGAAATAACGGGGTTAGAGTATCCTCGATGGTGAAAAATCGATGTTTT
1 GGTTGGAGTATCTCCTAAGAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTT
* *
3182631 GGAAATAAAATTGG
66 GAAAATAAAATCGG
* * * * * * *
3182645 GGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTACCCCCGATTGTGGAAAATTGATATTTT
1 GGTTGGAGTATCTCCTAAGAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTT
*
3182710 GAAAATAAAATCGA
66 GAAAATAAAATCGG
* * * *
3182724 GGTTGGAGTATCTCCTTAGAAATAACGGGGTTGGAGTATCCCCGATGGTGGAAAATCGGTATTTT
1 GGTTGGAGTATCTCCTAAGAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTT
3182789 AGAAAA-AAAA
66 -GAAAATAAAA
3182799 CATCAATGGA
Statistics
Matches: 197, Mismatches: 35, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
79 192 0.97
80 5 0.03
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCTCCTAAGAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTT
GAAAATAAAATCGG
Found at i:3182779 original size:158 final size:158
Alignment explanation
Indices: 3182487--3182781 Score: 428
Period size: 158 Copynumber: 1.9 Consensus size: 158
3182477 AAAATAACGA
* * * * *
3182487 GGTTGGAGTATCCCCTTACAAATAACGGGGTTGGAGCATCCTCGATTGTGAAAAATCGATGTTTT
1 GGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGCACCCCCGATTGTGAAAAATCGATATTTT
* * * *
3182552 CAAAATAAAATGGGGGTTGGAATATCTCATCGGAAATAACGGGGTTAGAGTATCCTCGATGGTGA
66 CAAAATAAAATCGAGGTTGGAATATCTCATCAGAAATAACGGGGTTAGAGTATCCCCGATGGTGA
3182617 AAAATCGATGTTTTGGAAATAAAATTGG
131 AAAATCGATGTTTTGGAAATAAAATTGG
* * *
3182645 GGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTACCCCCGATTGTGGAAAATTGATATTTT
1 GGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGCACCCCCGATTGTGAAAAATCGATATTTT
* * * * * *
3182710 GAAAATAAAATCGAGGTTGGAGTATCTCCTTAGAAATAACGGGGTTGGAGTATCCCCGATGGTGG
66 CAAAATAAAATCGAGGTTGGAATATCTCATCAGAAATAACGGGGTTAGAGTATCCCCGATGGTGA
3182775 AAAATCG
131 AAAATCG
3182782 GTATTTTAGA
Statistics
Matches: 119, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
158 119 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (158 bp):
GGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGCACCCCCGATTGTGAAAAATCGATATTTT
CAAAATAAAATCGAGGTTGGAATATCTCATCAGAAATAACGGGGTTAGAGTATCCCCGATGGTGA
AAAATCGATGTTTTGGAAATAAAATTGG
Found at i:3185788 original size:42 final size:42
Alignment explanation
Indices: 3185738--3185850 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 42
3185728 GTACGTCTTG
*
3185738 CTCTTTGAGGACAAAGAGAAAAAGAAAATGAAGTGTGTCCTA
1 CTCTTTGAGGACAAAGAGAAAAAGAAAATGAAGTGTGTCCCA
* * * * *
3185780 CTTTTTGAGAATAAAG-GAAAAGAAGGAAATGAAGTGTGTCCCG
1 CTCTTTGAGGACAAAGAG-AAA-AAGAAAATGAAGTGTGTCCCA
*
3185823 CTCTTTGAGGACAAAAGAGAAAAGGAAA
1 CTCTTTGAGGAC-AAAGAGAAAAAGAAA
3185851 TGAGTTCTGA
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
41 1 0.02
42 16 0.29
43 31 0.55
44 7 0.12
45 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.20
Consensus pattern (42 bp):
CTCTTTGAGGACAAAGAGAAAAAGAAAATGAAGTGTGTCCCA
Found at i:3185796 original size:77 final size:75
Alignment explanation
Indices: 3185640--3185800 Score: 179
Period size: 77 Copynumber: 2.1 Consensus size: 75
3185630 CTCTTTGTGC
* * *
3185640 ACAAAGGAAAGA-G-GTACGTCTTACTTTTCGAGGACAAAGGAAAAGAGAATGAAATAGGTCCTG
1 ACAAAGGAAAAAGGAGTACGTCTTACTTTTCGAGGACAAAGGAAAAGAAAATGAAATAGGTCCTA
3185703 CTTCTTGAAG
66 CTTCTTGAAG
* *
3185713 ACAAAGGAAAAAGGAGTACGTCTTGCTCTTT-GAGGACAAAGAGAAAAAGAAAATGAAGT-GTGT
1 ACAAAGGAAAAAGGAGTACGTCTTACT-TTTCGAGGACAAAG-G-AAAAGAAAATGAAATAG-GT
*
3185776 CCTACTTTTTG-AG
62 CCTACTTCTTGAAG
*
3185789 AATAAAGGAAAA
1 -ACAAAGGAAAA
3185801 GAAGGAAATG
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
73 11 0.15
74 1 0.01
75 21 0.28
76 7 0.09
77 34 0.46
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.22
Consensus pattern (75 bp):
ACAAAGGAAAAAGGAGTACGTCTTACTTTTCGAGGACAAAGGAAAAGAAAATGAAATAGGTCCTA
CTTCTTGAAG
Found at i:3185830 original size:43 final size:41
Alignment explanation
Indices: 3185737--3186010 Score: 138
Period size: 42 Copynumber: 6.8 Consensus size: 41
3185727 AGTACGTCTT
* *
3185737 GCTCTTTGAGGACAAAGAGAAAAAGAAAATGAAGTGTGTCCT
1 GCTCTTTGAGGACAAAGA-AAAAAGGAAATGAAGTGTGTCCC
* * * *
3185779 ACTTTTTGAGAATAAAGGAAAAGAAGGAAATGAAGTGTGTCCC
1 GCTCTTTGAGGACAAA-GAAAA-AAGGAAATGAAGTGTGTCCC
* *
3185822 GCTCTTTGAGGACAAAAGAGAAAAGGAAATG-A--GT-T-CT
1 GCTCTTTGAGGAC-AAAGAAAAAAGGAAATGAAGTGTGTCCC
* * * ** ** *
3185859 GATCTTTGACGACTAAG--GGAA--AAA-G-AGTACGTCCT
1 GCTCTTTGAGGACAAAGAAAAAAGGAAATGAAGTGTGTCCC
* * * ** *
3185894 ACTCTTCGAGGACAAAGGAAAAAAGGAAATAAAGTGCATCCT
1 GCTCTTTGAGGACAAA-GAAAAAAGGAAATGAAGTGTGTCCC
* * **
3185936 ACTCTTTGAGGACAAAGGGAAAAAATGGAAATGAAATGTGTCAT
1 GCTCTTTGAGGACAAA--GAAAAAA-GGAAATGAAGTGTGTCCC
* * *
3185980 GCTCTTTAAGGATAAAGGAAAAAGGAAATGA
1 GCTCTTTGAGGACAAAGAAAAAAGGAAATGA
3186011 GGAAAGTGTC
Statistics
Matches: 177, Mismatches: 39, Indels: 33
0.71 0.16 0.13
Matches are distributed among these distances:
31 2 0.01
32 3 0.02
34 3 0.02
35 13 0.07
36 4 0.02
37 12 0.07
38 3 0.02
39 2 0.01
40 3 0.02
41 9 0.05
42 53 0.30
43 41 0.23
44 29 0.16
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (41 bp):
GCTCTTTGAGGACAAAGAAAAAAGGAAATGAAGTGTGTCCC
Found at i:3185905 original size:157 final size:158
Alignment explanation
Indices: 3185718--3186011 Score: 389
Period size: 157 Copynumber: 1.9 Consensus size: 158
3185708 TGAAGACAAA
* * * * **
3185718 GGAAAAAGGAGTACGTCTTGCTCTTTGAGGACAAA-GAGAAAAAGAAAATGAAGTGTGTCCTACT
1 GGAAAAAGGAGTACGTCCTACTCTTCGAGGACAAAGGA-AAAAAGAAAATAAAGTGCATCCTACT
* * * * *
3185782 TTTTGAGAATAAA-GGAAAAGAA-GGAAATGAAGTGTGTCCCGCTCTTTGAGGACAAAAGAGAAA
65 CTTTGAGAACAAAGGGAAAA-AATGGAAATGAAATGTGTCACGCTCTTTAAGGACAAAAGA-AAA
3185845 AGGAAATGAGTTCTGATCTTTGACGACTAAG
128 AGGAAATGAGTTCTGATCTTTGACGACTAAG
*
3185876 GGAAAAA-GAGTACGTCCTACTCTTCGAGGACAAAGGAAAAAAGGAAATAAAGTGCATCCTACTC
1 GGAAAAAGGAGTACGTCCTACTCTTCGAGGACAAAGGAAAAAAGAAAATAAAGTGCATCCTACTC
* * * *
3185940 TTTGAGGACAAAGGGAAAAAATGGAAATGAAATGTGTCATGCTCTTTAAGGATAAAGGAAAAAGG
66 TTTGAGAACAAAGGGAAAAAATGGAAATGAAATGTGTCACGCTCTTTAAGGACAAAAGAAAAAGG
3186005 AAATGAG
131 AAATGAG
3186012 GAAAGTGTCC
Statistics
Matches: 117, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
157 71 0.61
158 46 0.39
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.21
Consensus pattern (158 bp):
GGAAAAAGGAGTACGTCCTACTCTTCGAGGACAAAGGAAAAAAGAAAATAAAGTGCATCCTACTC
TTTGAGAACAAAGGGAAAAAATGGAAATGAAATGTGTCACGCTCTTTAAGGACAAAAGAAAAAGG
AAATGAGTTCTGATCTTTGACGACTAAG
Found at i:3185985 original size:44 final size:42
Alignment explanation
Indices: 3185893--3186010 Score: 134
Period size: 44 Copynumber: 2.8 Consensus size: 42
3185883 GAGTACGTCC
* *
3185893 TACTCTTCGAGGACAAAGGAAAAAAGGAAAT-AAAGTGCATCC
1 TACTCTTTGAGGACAAAGGAAAAAAGGAAATGAAAGTG-ATCA
3185935 TACTCTTTGAGGACAAAGGGAAAAAATGGAAATGAAATGTG-TCA
1 TACTCTTTGAGGACAAA-GGAAAAAA-GGAAATGAAA-GTGATCA
* * *
3185979 TGCTCTTTAAGGATAAAGG-AAAAAGGAAATGA
1 TACTCTTTGAGGACAAAGGAAAAAAGGAAATGA
3186011 GGAAAGTGTC
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
41 8 0.12
42 21 0.31
43 10 0.15
44 22 0.33
45 3 0.04
46 3 0.04
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.20
Consensus pattern (42 bp):
TACTCTTTGAGGACAAAGGAAAAAAGGAAATGAAAGTGATCA
Found at i:3188808 original size:21 final size:21
Alignment explanation
Indices: 3188775--3188819 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3188765 TTGCAAGTTG
*
3188775 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3188797 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3188817 AAA
1 AAA
3188820 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3190643 original size:15 final size:15
Alignment explanation
Indices: 3190623--3190653 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3190613 TAAAAATGTC
*
3190623 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3190638 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3190653 C
1 C
3190654 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3192736 original size:20 final size:20
Alignment explanation
Indices: 3192737--3192774 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3192727 TTTCTTTGTA
3192737 TCTATGTATCGATACATTTT
1 TCTATGTATCGATACATTTT
*
3192757 TCTTTGTATCGATACATT
1 TCTATGTATCGATACATT
3192775 GTATCGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.50
Consensus pattern (20 bp):
TCTATGTATCGATACATTTT
Found at i:3192749 original size:28 final size:28
Alignment explanation
Indices: 3192709--3192766 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3192699 ATCTGGAAAT
3192709 TCTATGTATCGATACATTTTTCTTTGTA
1 TCTATGTATCGATACATTTTTCTTTGTA
3192737 TCTATGTATCGATACATTTTTCTTTGTA
1 TCTATGTATCGATACATTTTTCTTTGTA
3192765 TC
1 TC
3192767 GATACATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.16, G:0.10, T:0.53
Consensus pattern (28 bp):
TCTATGTATCGATACATTTTTCTTTGTA
Found at i:3192778 original size:13 final size:13
Alignment explanation
Indices: 3192760--3192824 Score: 112
Period size: 13 Copynumber: 5.0 Consensus size: 13
3192750 ACATTTTTCT
3192760 TTGTATCGATACA
1 TTGTATCGATACA
3192773 TTGTATCGATACA
1 TTGTATCGATACA
*
3192786 CTGTATCGATACA
1 TTGTATCGATACA
3192799 TTGTATCGATACA
1 TTGTATCGATACA
*
3192812 CTGTATCGATACA
1 TTGTATCGATACA
3192825 GGGTGATTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3192797 original size:26 final size:26
Alignment explanation
Indices: 3192761--3192824 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
3192751 CATTTTTCTT
3192761 TGTATCGATACATTGTATCGATACAC
1 TGTATCGATACATTGTATCGATACAC
3192787 TGTATCGATACATTGTATCGATACAC
1 TGTATCGATACATTGTATCGATACAC
3192813 TGTATCGATACA
1 TGTATCGATACA
3192825 GGGTGATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (26 bp):
TGTATCGATACATTGTATCGATACAC
Found at i:3194612 original size:14 final size:14
Alignment explanation
Indices: 3194595--3194630 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3194585 GGGGGAGAGA
*
3194595 AAATAGATATGTGC
1 AAATAAATATGTGC
*
3194609 AAATAAATTTGTGC
1 AAATAAATATGTGC
3194623 AAATAAAT
1 AAATAAAT
3194631 TTTTGATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.31
Consensus pattern (14 bp):
AAATAAATATGTGC
Found at i:3194631 original size:14 final size:14
Alignment explanation
Indices: 3194604--3194632 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3194594 AAAATAGATA
3194604 TGTGCAAATAAATT
1 TGTGCAAATAAATT
3194618 TGTGCAAATAAATT
1 TGTGCAAATAAATT
3194632 T
1 T
3194633 TTGATATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (14 bp):
TGTGCAAATAAATT
Found at i:3195409 original size:13 final size:13
Alignment explanation
Indices: 3195391--3195417 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3195381 TACAGCAAGT
3195391 ATGTATCGATACA
1 ATGTATCGATACA
3195404 ATGTATCGATACA
1 ATGTATCGATACA
3195417 A
1 A
3195418 AAAAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3196428 original size:62 final size:60
Alignment explanation
Indices: 3196172--3196991 Score: 750
Period size: 62 Copynumber: 13.3 Consensus size: 60
3196162 GCTTTCAGCG
* * **
3196172 TCCTACTCTTTGAGGAATAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAAAAAGGCA
* * * * *
3196232 TCCTACTCTTTGAGGACTAGAAGGTGACACCAACTCATGTGGGCTTT--TAAAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAAAAAGGCA
* * ** * * * * * * *
3196290 TTCTAG-TCTCTGAAAAATAAAAATGTGCCACTAGCTTGTATGGGCTTTGAAAAAATAAGGCA
1 TCCT-GCTCTTTGAGGACT-AAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAAAAAAGGCA
* * **
3196352 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAAATCATGTGGGCTTTGAAAGAAAAAAGGTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAA-AAAAAAGGCA
* * * * * **
3196414 TCCTGCTCCTTGAGGACTAAAGGGTACCACTACCTCGTGTGGGCTTTGAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAAAAAAGGCA
* * * *
3196475 TCTTGCTCTTTGAGGACTAAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGGCG
1 TCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAA-AAAAAGGCA
* * * * **
3196538 TCCTACTCTTTGAGGACTAAATGGTGCCACCAACTCGTGTAGCCTTTGAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAAAAAAGGCA
* * *
3196599 TCATGCTCTTTGAGGACTAAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAGAGTGC-
1 TCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAA-AAAAAG-GCA
* * * * **
3196662 -CTTGCTCTTTGAGGACTAAAAAGGTGCCACCTACTTGTGTGGCCTTTAAAAAGGAAAAGGTG
1 TCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAA--AAAAGGCA
* * *
3196724 TCCTGCTTTTTGAGGACTAAAATGTGCCACAAACTCGTGTGGGCTTTAAAAAGAAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAA-AAAAAGGCA
* * *
3196786 TCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAA--AAAAGGCA
* * * * * * * **
3196848 TCCTACTCTTCGAGGATTGAAAGGTGCTATCAACTCATGTAAGCTTTAAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAA--AAAAGGCA
* * * ** *
3196910 TCCTACTCTTTGACGACTAAAATGTGCCATTAACTCATGTGGGCTTTAAAAGAAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAA-AAAAAGGCA
3196971 TCCTGCTCTTTGAGGACTAAA
1 TCCTGCTCTTTGAGGACTAAA
3196992 GGGCTAAAAG
Statistics
Matches: 618, Mismatches: 121, Indels: 41
0.79 0.16 0.05
Matches are distributed among these distances:
58 19 0.03
59 21 0.03
60 44 0.07
61 108 0.17
62 375 0.61
63 48 0.08
64 3 0.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAAAAAGGCA
Found at i:3196555 original size:124 final size:123
Alignment explanation
Indices: 3196172--3196991 Score: 852
Period size: 124 Copynumber: 6.7 Consensus size: 123
3196162 GCTTTCAGCG
* *
3196172 TCCTACTCTTTGAGGAATAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGG-AAAGGCATCCT
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACTAACTCGTGTGGGCTTTAAAAGGAAAAGGCATCCT
* * * *
3196236 ACTCTTTGAGGACTAGAAGGTGACACCAACTCATGTGGGCTTT---TA-AAAAAGGCA
66 GCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCA
* * * ** * * * * *
3196290 TTCTAGTCTCTGAAAAATAAAAATGTGCCACTAGCTTGTATGGGCTTTGAAAA--AATAAGGCAT
1 TCCTACTCTTTGAGGACT-AAAAGGTGCCACTAACTCGTGTGGGCTTT-AAAAGGAA-AAGGCAT
* * **
3196353 CCTGCTCTTTGAGGACTAAAAGGTGCCACCAAATCATGTGGGCTTT-GAAAGAAAAAAGGTG
63 CCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAG-AAAAAGGCA
* * * * * * *
3196414 TCCTGCTCCTTGAGGACTAAAGGGTACCACTACCTCGTGTGGGCTTTGAAAGGAAAAGGCATCTT
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACTAACTCGTGTGGGCTTTAAAAGGAAAAGGCATCCT
* ** *
3196479 GCTCTTTGAGGACTAAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAGGCG
66 GCTCTTTGAGGACT-AAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCA
* * * * * *
3196538 TCCTACTCTTTGAGGACTAAATGGTGCCACCAACTCGTGTAGCCTTTGAAAGGAAAAGGCATCAT
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACTAACTCGTGTGGGCTTTAAAAGGAAAAGGCATCCT
* * * *
3196603 GCTCTTTGAGGACTAAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAGAGTGC-
66 GCTCTTTGAGGACT-AAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAG-GCA
* * * * **
3196662 -CTTGCTCTTTGAGGACTAAAAAGGTGCCACCT-ACTTGTGTGGCCTTTAAAAAGGAAAAGGTGT
1 TCCTACTCTTTGAGGACT-AAAAGGTGCCA-CTAACTCGTGTGGGCTTT-AAAAGGAAAAGGCAT
* * * *
3196725 CCTGCTTTTTGAGGACTAAAATGTGCCACAAACTCGTGTGGGCTTTAAAAAGAAAAAGGCA
63 CCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCA
* * *
3196786 TCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGGAAAAGGCGTCC
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACTAACTCGTGTGGGCTTT-AAAAGGAAAAGGCATCC
* * * * * * ** *
3196851 TACTCTTCGAGGATTGAAAGGTGCTATCAACTCATGTAAGCTTTAAAAAGGAAAAGGCA
65 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCA
* * * * *
3196910 TCCTACTCTTTGACGACTAAAATGTGCCATTAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCT
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACTAACTCGTGTGGGCTTTAAAAGGAAAAGGCATCCT
3196975 GCTCTTTGAGGACTAAA
66 GCTCTTTGAGGACTAAA
3196992 GGGCTAAAAG
Statistics
Matches: 582, Mismatches: 101, Indels: 33
0.81 0.14 0.05
Matches are distributed among these distances:
118 13 0.02
119 25 0.04
120 53 0.09
122 4 0.01
123 93 0.16
124 345 0.59
125 49 0.08
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (123 bp):
TCCTACTCTTTGAGGACTAAAAGGTGCCACTAACTCGTGTGGGCTTTAAAAGGAAAAGGCATCCT
GCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCA
Found at i:3196587 original size:186 final size:185
Alignment explanation
Indices: 3196169--3196994 Score: 847
Period size: 186 Copynumber: 4.5 Consensus size: 185
3196159 TAAGCTTTCA
* * **
3196169 GCGTCCTACTCTTTGAGGAATAAAAGGTGCCACCAACTCGTGTGGGCTTTAAA-AGGAAAGGCAT
1 GCGTCCTACTCTTTGAGGACTAAATGGTGCCACCAACTCGTGTGGGCTTTAAAGAAAAAAGGCAT
* * *
3196233 CCTACTCTTTGAGGACTAGAA-GGTGA-CACCAACTCATGTGGGCTTT-TAA--AAAAGGCATTC
66 CCTGCTCTTTGAGGACTA-AAGGGT-ACCACCAACTCGTGTGGGCTTTGAAAGGAAAAGGCA-TC
* * ** * * * * * *
3196293 TAG-TCTCTGAAAAATAAAAATGTGCCACTAGCTTGTATGGGCTTTGAAAA-AATAAG
128 TTGCTCTTTGAGGACTAAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAG
* * * * * **
3196349 GCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAAATCATGTGGGCTTTGAAAGAAAAAAGGTG
1 GCGTCCTACTCTTTGAGGACTAAATGGTGCCACCAACTCGTGTGGGCTTT-AAAGAAAAAAGGCA
* * *
3196414 TCCTGCTCCTTGAGGACTAAAGGGTACCACTACCTCGTGTGGGCTTTGAAAGGAAAAGGCATCTT
65 TCCTGCTCTTTGAGGACTAAAGGGTACCACCAACTCGTGTGGGCTTTGAAAGGAAAAGGCATCTT
3196479 GCTCTTTGAGGACTAAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAG
130 GCTCTTTGAGGACTAAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAG
* * *
3196535 GCGTCCTACTCTTTGAGGACTAAATGGTGCCACCAACTCGTGTAGCCTTTGAAAG-GAAAAGGCA
1 GCGTCCTACTCTTTGAGGACTAAATGGTGCCACCAACTCGTGTGGGCTTT-AAAGAAAAAAGGCA
* * * *
3196599 TCATGCTCTTTGAGGACTAAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAGAGTGC--
65 TCCTGCTCTTTGAGGACT-AAAGGGTACCACCAACTCGTGTGGGCTTTG-AAAGGAAAAG-GCAT
* *
3196662 CTTGCTCTTTGAGGACTAAAAAGGTGCCACCTA-CTTGTGTGGCCTTTAAAAAGGAAAAG
127 CTTGCTCTTTGAGGACTAAAAAGGTGCCACC-AGCTTGTGTGGGCTTTAAAAAGAAAAAG
* * * * *
3196721 GTGTCCTGCTTTTTGAGGACTAAAAT-GTGCCACAAACTCGTGTGGGCTTTAAAAAGAAAAAGGC
1 GCGTCCTACTCTTTGAGGACT-AAATGGTGCCACCAACTCGTGTGGGCTTTAAAGA-AAAAAGGC
* * * *
3196785 ATCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGGAAAAGGCGTC
64 ATCCTGCTCTTTGAGGACTAAAGGGTACCACCAACTCGTGTGGGCTTT-GAAAGGAAAAGGCATC
* * * ** * * * ** ** *
3196850 CTACTCTTCGAGGA-TTGAAAGGTGCTATCAACTCATGTAAGCTTTAAAAAGGAAAAG
128 TTGCTCTTTGAGGACTAAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAG
* * ** *
3196907 GCATCCTACTCTTTGACGACTAAAAT-GTGCCATTAACTCATGTGGGCTTTAAA-AGAAAAAGGC
1 GCGTCCTACTCTTTGAGGACT-AAATGGTGCCACCAACTCGTGTGGGCTTTAAAGA-AAAAAGGC
3196970 ATCCTGCTCTTTGAGGACTAAAGGG
64 ATCCTGCTCTTTGAGGACTAAAGGG
3196995 CTAAAAGGGG
Statistics
Matches: 548, Mismatches: 78, Indels: 35
0.83 0.12 0.05
Matches are distributed among these distances:
180 45 0.08
181 6 0.01
182 43 0.08
183 2 0.00
184 4 0.01
185 109 0.20
186 287 0.52
187 50 0.09
188 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (185 bp):
GCGTCCTACTCTTTGAGGACTAAATGGTGCCACCAACTCGTGTGGGCTTTAAAGAAAAAAGGCAT
CCTGCTCTTTGAGGACTAAAGGGTACCACCAACTCGTGTGGGCTTTGAAAGGAAAAGGCATCTTG
CTCTTTGAGGACTAAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAG
Found at i:3200312 original size:79 final size:78
Alignment explanation
Indices: 3200214--3200468 Score: 241
Period size: 79 Copynumber: 3.2 Consensus size: 78
3200204 ACTCAAATCT
* * * * *
3200214 CGATTTAATTCCTAAAACATCAATTTTCCACAATTAGGGATACGCCAACCCTATTATTTCTGAGG
1 CGATTTTATTTCTAAAACATCGATTTTCCACAATT-GGGATACTCCAACCCTGTTATTTCTGAGG
3200279 GGATACTCCAAACC
65 GGATACTCCAAACC
* * * * * *
3200293 CGGTTTTCTTTCTAAAACATCGATATTCTCACAATTGGGGATACTTCAACCCTGTTATTTCCGAA
1 CGATTTTATTTCTAAAACATCGATTTTC-CACAATT-GGGATACTCCAACCCTGTTATTTCTGAG
* *
3200358 GGGATACTCTAACCC
64 GGGATACTCCAAACC
* * *
3200373 CGATTTTATTT-TCAAAACACCGATTTTACATC-ATTGAGGATACTCCAA-CCTCGCTATTTCTG
1 CGATTTTATTTCT-AAAACATCGATTTTCCA-CAATTG-GGATACTCCAACCCT-GTTATTTCTG
3200435 AGGGGATACT-CAAACC
62 AGGGGATACTCCAAACC
*
3200451 TC-ATTTTTATCTCTAAAA
1 -CGA-TTTTATTTCTAAAA
3200469 TATTAAATTT
Statistics
Matches: 142, Mismatches: 26, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
78 9 0.06
79 67 0.47
80 66 0.46
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (78 bp):
CGATTTTATTTCTAAAACATCGATTTTCCACAATTGGGATACTCCAACCCTGTTATTTCTGAGGG
GATACTCCAAACC
Found at i:3207115 original size:13 final size:13
Alignment explanation
Indices: 3207097--3207122 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3207087 ATGGTGGTTT
3207097 TGTATCGATACAA
1 TGTATCGATACAA
3207110 TGTATCGATACAA
1 TGTATCGATACAA
3207123 AATTTATATA
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:3207912 original size:62 final size:62
Alignment explanation
Indices: 3207835--3207974 Score: 162
Period size: 62 Copynumber: 2.3 Consensus size: 62
3207825 GAGAAGAGTA
* *
3207835 CCAATATGATGATTCAATGTC-AGTGACATT-GGACTTAAAGATGCA-AAGAAATGATAAAGTTG
1 CCAATATGATGATTCAATGGCTAGTGACATTAGG-CTTAAAGATG-AGAAG-AATGATAAAGGTG
* * * *
3207897 CCAATATGTTGATTC-ATGGCTAGTGATATTAGGCTTGAATATGAGAAGAATGATAAAGGTG
1 CCAATATGATGATTCAATGGCTAGTGACATTAGGCTTAAAGATGAGAAGAATGATAAAGGTG
*
3207958 CCAATATGCTGATTCAA
1 CCAATATGATGATTCAA
3207975 GGCCAACGAT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
61 31 0.46
62 34 0.51
63 2 0.03
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.29
Consensus pattern (62 bp):
CCAATATGATGATTCAATGGCTAGTGACATTAGGCTTAAAGATGAGAAGAATGATAAAGGTG
Found at i:3208009 original size:61 final size:61
Alignment explanation
Indices: 3207884--3208009 Score: 153
Period size: 61 Copynumber: 2.1 Consensus size: 61
3207874 GATGCAAAGA
* * * * ** * *
3207884 AATGATAAAGTTGCCAATATGTTGATTCATGGCTAGTGATATTAGGCTTGAATATGAGAAG
1 AATGATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTAGGCTTAAAAATGAGAAG
* * *
3207945 AATGATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAAAATGCGAGG
1 AATGATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTAGGCTTAAAAATGAGAAG
3208006 AATG
1 AATG
3208010 CCAATGTGCT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (61 bp):
AATGATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTAGGCTTAAAAATGAGAAG
Found at i:3209048 original size:20 final size:20
Alignment explanation
Indices: 3209025--3209099 Score: 89
Period size: 20 Copynumber: 3.6 Consensus size: 20
3209015 CGTTGGACTC
*
3209025 AATGTATAGATACTATTCAG
1 AATGTATCGATACTATTCAG
*
3209045 AATGTATCGATAC-ATGAACAG
1 AATGTATCGATACTAT--TCAG
*
3209066 TGATGTATCGATACTATTCAG
1 -AATGTATCGATACTATTCAG
3209087 AATGTATCGATAC
1 AATGTATCGATAC
3209100 ATGAACAGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.04
20 24 0.52
21 6 0.13
22 12 0.26
23 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACTATTCAG
Found at i:3209072 original size:22 final size:22
Alignment explanation
Indices: 3209046--3209112 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
3209036 ACTATTCAGA
3209046 ATGTATCGATACATGAACAGTG
1 ATGTATCGATACATGAACAGTG
* *
3209068 ATGTATCGATAC-T-ATTCAG-A
1 ATGTATCGATACATGA-ACAGTG
3209088 ATGTATCGATACATGAACAGTG
1 ATGTATCGATACATGAACAGTG
3209110 ATG
1 ATG
3209113 AATAGTGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 13 0.35
21 8 0.22
22 16 0.43
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (22 bp):
ATGTATCGATACATGAACAGTG
Found at i:3209072 original size:42 final size:42
Alignment explanation
Indices: 3209026--3209117 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
3209016 GTTGGACTCA
3209026 ATGTATAGATACTATTCAGAATGTATCGATACATGAACAGTG
1 ATGTATAGATACTATTCAGAATGTATCGATACATGAACAGTG
*
3209068 ATGTATCGATACTATTCAGAATGTATCGATACATGAACAGTG
1 ATGTATAGATACTATTCAGAATGTATCGATACATGAACAGTG
*
3209110 ATGAATAG
1 ATGTATAG
3209118 TGATAAATAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (42 bp):
ATGTATAGATACTATTCAGAATGTATCGATACATGAACAGTG
Found at i:3212231 original size:21 final size:21
Alignment explanation
Indices: 3212206--3212260 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3212196 CACTTGCAAC
*
3212206 TCATTTCTTTTCTCCTCTAAT
1 TCATTTATTTTCTCCTCTAAT
**
3212227 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCCTCTAAT
* *
3212248 TCACTTAATTTCT
1 TCATTTATTTTCT
3212261 TTTCAAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (21 bp):
TCATTTATTTTCTCCTCTAAT
Found at i:3212261 original size:21 final size:21
Alignment explanation
Indices: 3212221--3212264 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3212211 TCTTTTCTCC
* *
3212221 TCTAATTCATTTATTTTCTTT
1 TCTAATTCACTTAATTTCTTT
3212242 TCTAATTCACTTAATTTCTTT
1 TCTAATTCACTTAATTTCTTT
3212263 TC
1 TC
3212265 AAGAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTAATTCACTTAATTTCTTT
Found at i:3212725 original size:21 final size:21
Alignment explanation
Indices: 3212686--3212726 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3212676 AGCCATTTCT
* *
3212686 TCATTTTCATCAACCTTTTGG
1 TCATCTTCATCAACATTTTGG
*
3212707 TCATCTTCATCATCATTTTG
1 TCATCTTCATCAACATTTTG
3212727 AACAGTTGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.24, G:0.07, T:0.49
Consensus pattern (21 bp):
TCATCTTCATCAACATTTTGG
Found at i:3214580 original size:20 final size:20
Alignment explanation
Indices: 3214557--3214629 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3214547 ACAATTCAAA
3214557 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3214577 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3214598 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3214618 GTATCGATACAT
1 GTATCGATACAT
3214630 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3214601 original size:21 final size:21
Alignment explanation
Indices: 3214575--3214650 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3214565 ACATGTTGCA
3214575 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3214596 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
3214616 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
3214637 ATGTATCGATACAT
1 ATGTATCGATACAT
3214651 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3214608 original size:41 final size:41
Alignment explanation
Indices: 3214557--3214650 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3214547 ACAATTCAAA
*
3214557 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3214598 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3214639 GTATCGATACAT
1 GTATCGATACAT
3214651 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3214707 original size:13 final size:13
Alignment explanation
Indices: 3214689--3214714 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3214679 TACAGCAAGT
3214689 ATGTATCGATACA
1 ATGTATCGATACA
3214702 ATGTATCGATACA
1 ATGTATCGATACA
3214715 CAAAAAATTG
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:3218796 original size:15 final size:15
Alignment explanation
Indices: 3218776--3218806 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3218766 TAAAAATGTC
*
3218776 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3218791 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3218806 C
1 C
3218807 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3220890 original size:20 final size:20
Alignment explanation
Indices: 3220862--3220900 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3220852 CATCTGGAAA
*
3220862 TTCTATGTATTGATACATTT
1 TTCTATGTATCGATACATTT
*
3220882 TTCTTTGTATCGATACATT
1 TTCTATGTATCGATACATT
3220901 GTATCGATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54
Consensus pattern (20 bp):
TTCTATGTATCGATACATTT
Found at i:3220904 original size:13 final size:13
Alignment explanation
Indices: 3220886--3220924 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3220876 ACATTTTTCT
3220886 TTGTATCGATACA
1 TTGTATCGATACA
3220899 TTGTATCGATACA
1 TTGTATCGATACA
*
3220912 CTGTATCGATACA
1 TTGTATCGATACA
3220925 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3223350 original size:20 final size:20
Alignment explanation
Indices: 3223327--3223399 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3223317 ACAATTCAAA
3223327 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3223347 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3223368 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3223388 GTATCGATACAT
1 GTATCGATACAT
3223400 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3223371 original size:21 final size:21
Alignment explanation
Indices: 3223345--3223420 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3223335 ACATGTTGCA
3223345 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3223366 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
3223386 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
3223407 ATGTATCGATACAT
1 ATGTATCGATACAT
3223421 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3223378 original size:41 final size:41
Alignment explanation
Indices: 3223327--3223420 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3223317 ACAATTCAAA
*
3223327 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3223368 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3223409 GTATCGATACAT
1 GTATCGATACAT
3223421 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3223477 original size:13 final size:13
Alignment explanation
Indices: 3223459--3223484 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3223449 TACAGCAAGT
3223459 ATGTATCGATACA
1 ATGTATCGATACA
3223472 ATGTATCGATACA
1 ATGTATCGATACA
3223485 CAAAAAATTG
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:3224365 original size:20 final size:20
Alignment explanation
Indices: 3224340--3224411 Score: 135
Period size: 20 Copynumber: 3.6 Consensus size: 20
3224330 ATGAACAGTG
3224340 ATGTATCGATACTATTCAGA
1 ATGTATCGATACTATTCAGA
*
3224360 ATGTATCGATACTATTTAGA
1 ATGTATCGATACTATTCAGA
3224380 ATGTATCGATACTATTCAGA
1 ATGTATCGATACTATTCAGA
3224400 ATGTATCGATAC
1 ATGTATCGATAC
3224412 ATGAACAGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACTATTCAGA
Found at i:3224431 original size:10 final size:10
Alignment explanation
Indices: 3224412--3224442 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3224402 GTATCGATAC
*
3224412 ATGAACAGTG
1 ATGAATAGTG
3224422 ATGAATAGTG
1 ATGAATAGTG
3224432 ATGAATAGTG
1 ATGAATAGTG
3224442 A
1 A
3224443 AAAATGAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:3224961 original size:52 final size:52
Alignment explanation
Indices: 3224854--3224982 Score: 170
Period size: 52 Copynumber: 2.5 Consensus size: 52
3224844 GATGACAAAG
** *
3224854 GTGCCAATGTGCCAATTCAAGGCCAGCAACATTGGACTTAAAAATGAGATGA
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAAATGAGAGGA
* *
3224906 GTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGACTTAAAGATGA-AGGAA
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAAATGAGAGG-A
* * *
3224958 GTGCTAATATGCTGATTCAGGGCCA
1 GTGCCAATGTGCTGATTCAAGGCCA
3224983 ATGGCCTTAG
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
51 2 0.03
52 65 0.97
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (52 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAAATGAGAGGA
Found at i:3225428 original size:33 final size:33
Alignment explanation
Indices: 3225383--3225470 Score: 149
Period size: 33 Copynumber: 2.7 Consensus size: 33
3225373 AACAAAAAAG
*
3225383 TGCCACCGACTTGTGTGGGCTTCTGAGAAAGGA
1 TGCCACCAACTTGTGTGGGCTTCTGAGAAAGGA
*
3225416 TGCCACCAACTTGTGTGGGCTTTTGAGAAAGGA
1 TGCCACCAACTTGTGTGGGCTTCTGAGAAAGGA
*
3225449 TGCCACCAACTTATGTGGGCTT
1 TGCCACCAACTTGTGTGGGCTT
3225471 AAAAGGATGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (33 bp):
TGCCACCAACTTGTGTGGGCTTCTGAGAAAGGA
Found at i:3226591 original size:24 final size:23
Alignment explanation
Indices: 3226564--3226644 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 23
3226554 CATTTGGACC
3226564 ATTTTTTTTGATGATTTTTTTAAA
1 ATTTTTTTTGATGATTTTTTT-AA
3226588 ATTTTTTTTGATTTGATTTTTTT-A
1 ATTTTTTTTGA--TGATTTTTTTAA
*
3226612 TTTTTTGATTTGATG-TTTTTTTAA
1 ATTTTT--TTTGATGATTTTTTTAA
*
3226636 TTTTTTTTT
1 ATTTTTTTT
3226645 ACGAAGGACC
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
22 3 0.06
23 7 0.14
24 26 0.51
26 15 0.29
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (23 bp):
ATTTTTTTTGATGATTTTTTTAA
Found at i:3226604 original size:26 final size:25
Alignment explanation
Indices: 3226564--3226643 Score: 91
Period size: 26 Copynumber: 3.4 Consensus size: 25
3226554 CATTTGGACC
3226564 ATTTTTTTTGA--TGATTTTTTTAAA
1 ATTTTTTTTGATTTGATTTTTTT-AA
3226588 ATTTTTTTTGATTTGATTTTTTT--
1 ATTTTTTTTGATTTGATTTTTTTAA
*
3226611 A--TTTTTTGATTTGATGTTTTTTTA
1 ATTTTTTTTGATTTGAT-TTTTTTAA
3226635 ATTTTTTTT
1 ATTTTTTTT
3226644 TACGAAGGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
21 14 0.29
22 6 0.12
23 1 0.02
24 12 0.24
26 16 0.33
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (25 bp):
ATTTTTTTTGATTTGATTTTTTTAA
Found at i:3226615 original size:21 final size:23
Alignment explanation
Indices: 3226591--3226641 Score: 79
Period size: 21 Copynumber: 2.3 Consensus size: 23
3226581 TTTTAAAATT
3226591 TTTTTTGATTTGA-TTTTTTT-A
1 TTTTTTGATTTGAGTTTTTTTAA
3226612 TTTTTTGATTTGATGTTTTTTTAA
1 TTTTTTGATTTGA-GTTTTTTTAA
3226636 TTTTTT
1 TTTTTT
3226642 TTTACGAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.48
23 7 0.26
24 7 0.26
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (23 bp):
TTTTTTGATTTGAGTTTTTTTAA
Found at i:3241195 original size:20 final size:19
Alignment explanation
Indices: 3241127--3241205 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 19
3241117 AAAAACCCAA
* *
3241127 AATGTATCGATACAATGAG
1 AATGTATCGATACATTTAG
3241146 AAGTGTATCGATACAATTGTAAG
1 AA-TGTATCGATAC-ATT-T-AG
*
3241169 CATGTATCGATACATTTAG
1 AATGTATCGATACATTTAG
*
3241188 TAATGTATTGATACATTT
1 -AATGTATCGATACATTT
3241206 CCTTGGCAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 4 0.08
20 27 0.54
21 5 0.10
22 11 0.22
23 3 0.06
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (19 bp):
AATGTATCGATACATTTAG
Found at i:3241245 original size:13 final size:13
Alignment explanation
Indices: 3241229--3241253 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3241219 TAAGGTGGTT
3241229 TTGTATCGATACG
1 TTGTATCGATACG
3241242 TTGTATCGATAC
1 TTGTATCGATAC
3241254 AAAACTTATG
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:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACG
Found at i:3254470 original size:28 final size:27
Alignment explanation
Indices: 3254401--3254473 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 27
3254391 TAAAGCCTGG
* *
3254401 GGTTGGAGTATCCCCTCG-GAAGTAACGG
1 GGTTGGAGTAT--CCTCGAGAAATAACGA
3254429 GGTTGGAGTATCCTCGATGAAATAACGA
1 GGTTGGAGTATCCTCGA-GAAATAACGA
3254457 GGTTGGAGTATCCTCGA
1 GGTTGGAGTATCCTCGA
3254474 CTGTGAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 5 0.12
28 36 0.88
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.25
Consensus pattern (27 bp):
GGTTGGAGTATCCTCGAGAAATAACGA
Found at i:3254556 original size:53 final size:54
Alignment explanation
Indices: 3254478--3254580 Score: 172
Period size: 53 Copynumber: 1.9 Consensus size: 54
3254468 CCTCGACTGT
* * *
3254478 GAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAG
1 GAAAAATTGGTAGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTAAAG
3254532 GAAAAATTGGT-GTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
1 GAAAAATTGGTAGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
3254581 GTGGAGAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 35 0.76
54 11 0.24
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (54 bp):
GAAAAATTGGTAGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTAAAG
Found at i:3256929 original size:33 final size:33
Alignment explanation
Indices: 3256867--3256933 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
3256857 AAAATTTCCA
***
3256867 AATGTATCGATACAAAGATCCATGCATCGATAC
1 AATGTATCGATACAAAGAAAAATGCATCGATAC
* *
3256900 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGCATCGATAC
3256933 A
1 A
3256934 TTTCCTTGGC
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:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGCATCGATAC
Found at i:3256977 original size:19 final size:18
Alignment explanation
Indices: 3256953--3257020 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
3256943 CAGTAGCTAA
3256953 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3256972 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3256987 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
3257004 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3257021 TTGTTGAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3256993 original size:13 final size:13
Alignment explanation
Indices: 3256975--3256999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3256965 ACAATACTTA
3256975 TGTATCGATACAT
1 TGTATCGATACAT
3256988 TGTATCGATACA
1 TGTATCGATACA
3257000 AAACTTATGT
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:3256997 original size:32 final size:32
Alignment explanation
Indices: 3256956--3257018 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3256946 TAGCTAATTA
*
3256956 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
3256988 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3257019 AATTGTTGAG
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Done.