Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 203 of 226
Found at i:64260208 original size:26 final size:25
Alignment explanation
Indices: 64260155--64260215 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
64260145 CAATAATTTT
**
64260155 ATATATTATATAATAAAACCCATGC
1 ATATATTATATAATAAAACCCACAC
* *
64260180 ATATATGTATATAGTAAGACCCACAC
1 ATATAT-TATATAATAAAACCCACAC
*
64260206 ATATAATATA
1 ATATATTATA
64260216 ATTTATGTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.31
Consensus pattern (25 bp):
ATATATTATATAATAAAACCCACAC
Found at i:64262162 original size:31 final size:31
Alignment explanation
Indices: 64262127--64262193 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
64262117 GACAGTTTTC
64262127 CTTTTCCTTCAAAGTATTTCTTTAATTCTTT
1 CTTTTCCTTCAAAGTATTTCTTTAATTCTTT
*
64262158 CTTTTCTTTCAAAGTATTTCTTTAATTCTTT
1 CTTTTCCTTCAAAGTATTTCTTTAATTCTTT
64262189 CTTTT
1 CTTTT
64262194 TCTTAAGTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.18, G:0.03, T:0.61
Consensus pattern (31 bp):
CTTTTCCTTCAAAGTATTTCTTTAATTCTTT
Found at i:64263185 original size:20 final size:21
Alignment explanation
Indices: 64263139--64263186 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
64263129 TTTTGTTAGT
*
64263139 CTTTGTGGCATTCTGATACGGC
1 CTTTGTGGCATTCTGATAC-AC
*
64263161 CTTTGTGGCATTCTGTTA-AC
1 CTTTGTGGCATTCTGATACAC
64263181 CTTTGT
1 CTTTGT
64263187 AACATTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
22 17 0.71
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (21 bp):
CTTTGTGGCATTCTGATACAC
Found at i:64264193 original size:31 final size:31
Alignment explanation
Indices: 64264155--64264216 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
64264145 AGGCAAATTA
64264155 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
64264186 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
64264217 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:64269774 original size:13 final size:13
Alignment explanation
Indices: 64269755--64269786 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
64269745 AGGTAGGCAA
64269755 CTTTTTTTTTGCG
1 CTTTTTTTTTGCG
*
64269768 GTTTTTTTTTGCG
1 CTTTTTTTTTGCG
64269781 CTTTTT
1 CTTTTT
64269787 GCTTTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (13 bp):
CTTTTTTTTTGCG
Found at i:64269801 original size:28 final size:29
Alignment explanation
Indices: 64269769--64269832 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
64269759 TTTTTTGCGG
64269769 TTTTTTTTTGCG-CTTTT-TGCTTTTTCTT
1 TTTTTTTTTG-GTCTTTTGTGCTTTTTCTT
* *
64269797 TTTTTTTTTGGTTTTTTTGTGCTTTTTGTT
1 TTTTTTTTTGG-TCTTTTGTGCTTTTTCTT
64269827 TTTTTT
1 TTTTTT
64269833 AAAGAATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 1 0.03
28 10 0.32
29 4 0.13
30 16 0.52
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (29 bp):
TTTTTTTTTGGTCTTTTGTGCTTTTTCTT
Found at i:64269811 original size:13 final size:14
Alignment explanation
Indices: 64269756--64269814 Score: 54
Period size: 13 Copynumber: 4.4 Consensus size: 14
64269746 GGTAGGCAAC
*
64269756 TTTTTTTTTGCG-G
1 TTTTTTTTTGCGTT
64269769 TTTTTTTTTGCGCTT
1 TTTTTTTTTGCG-TT
*
64269784 TTTGCTTTTT-C-TT
1 TTT-TTTTTTGCGTT
64269797 TTTTTTTTTG-GTT
1 TTTTTTTTTGCGTT
64269810 TTTTT
1 TTTTT
64269815 GTGCTTTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
12 5 0.13
13 24 0.63
15 4 0.11
16 5 0.13
ACGTcount: A:0.00, C:0.08, G:0.14, T:0.78
Consensus pattern (14 bp):
TTTTTTTTTGCGTT
Found at i:64269831 original size:9 final size:9
Alignment explanation
Indices: 64269782--64269832 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
64269772 TTTTTTGCGC
64269782 TTTTTGCTTT
1 TTTTTG-TTT
64269792 TTCTTT-TTT
1 TT-TTTGTTT
*
64269801 TTTTTGGTT
1 TTTTTGTTT
**
64269810 TTTTTGTGC
1 TTTTTGTTT
64269819 TTTTTGTTT
1 TTTTTGTTT
64269828 TTTTT
1 TTTTT
64269833 AAAGAATAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
8 3 0.09
9 25 0.76
10 2 0.06
11 3 0.09
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:64270385 original size:31 final size:31
Alignment explanation
Indices: 64270347--64270408 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
64270337 AGGCAAATTA
64270347 CAAGAGTAATTGAACCCTAATAAAACTCTTT
1 CAAGAGTAATTGAACCCTAATAAAACTCTTT
*
64270378 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAACCCTAATAAAACTCTTT
64270409 AAAATTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.31
Consensus pattern (31 bp):
CAAGAGTAATTGAACCCTAATAAAACTCTTT
Found at i:64276258 original size:2 final size:2
Alignment explanation
Indices: 64276251--64276282 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
64276241 TCTTTAAATC
64276251 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64276283 TANNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64276441 original size:2 final size:2
Alignment explanation
Indices: 64276429--64276468 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
64276419 TAAATTACTT
64276429 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64276469 TATTAAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64276782 original size:2 final size:2
Alignment explanation
Indices: 64276775--64276808 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
64276765 TTCTGTAAAT
64276775 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64276809 AATTTATCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64278937 original size:22 final size:23
Alignment explanation
Indices: 64278878--64278962 Score: 59
Period size: 22 Copynumber: 3.8 Consensus size: 23
64278868 TCTTCTTTCG
* * *
64278878 GAGAATATTCACTGTTCATGTTG
1 GAGAATATTCACTGTTCAAGCTA
***
64278901 GAGAAT-TTTGTTGTTCAAGCTA
1 GAGAATATTCACTGTTCAAGCTA
* *
64278923 GAGAAT-TTTACTGTTCATCGC-A
1 GAGAATATTCACTGTTCA-AGCTA
*
64278945 GAGAATCTTCACTGTTCA
1 GAGAATATTCACTGTTCA
64278963 TTCTCATTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
22 32 0.64
23 18 0.36
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (23 bp):
GAGAATATTCACTGTTCAAGCTA
Found at i:64282764 original size:24 final size:24
Alignment explanation
Indices: 64282736--64282793 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
64282726 AAAATTAAAA
64282736 GAAAAGAAAAATAAT-GAAGAAGAG
1 GAAAAGAAAAAT-ATCGAAGAAGAG
* *
64282760 GAAAAAGAAAAGTATCGAAGAAGAT
1 G-AAAAGAAAAATATCGAAGAAGAG
*
64282785 GAGAAGAAA
1 GAAAAGAAA
64282794 CTAAGGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.64, C:0.02, G:0.26, T:0.09
Consensus pattern (24 bp):
GAAAAGAAAAATATCGAAGAAGAG
Found at i:64291546 original size:56 final size:50
Alignment explanation
Indices: 64291328--64291576 Score: 309
Period size: 50 Copynumber: 4.8 Consensus size: 50
64291318 GATAATAACA
* * ** * *
64291328 TGCCAAAGCCCTGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
64291379 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
64291429 TGCCAATGCCATGACCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
64291479 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-CGG
*
64291534 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
64291577 TTACCCAAAT
Statistics
Matches: 172, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 94 0.55
51 32 0.19
53 3 0.02
54 1 0.01
55 2 0.01
56 40 0.23
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:64291692 original size:13 final size:13
Alignment explanation
Indices: 64291671--64291702 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
64291661 GCTTGGATCA
*
64291671 TCATCAAATAAAT
1 TCATAAAATAAAT
64291684 TCATAAAATAAAT
1 TCATAAAATAAAT
64291697 TCATAA
1 TCATAA
64291703 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:64291949 original size:30 final size:30
Alignment explanation
Indices: 64291914--64291971 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
64291904 CCTCGACTCT
*
64291914 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
64291944 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
64291972 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:64293436 original size:17 final size:17
Alignment explanation
Indices: 64293398--64293430 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
64293388 CACTAACATG
*
64293398 AAAATGTAATGACAATA
1 AAAATGCAATGACAATA
64293415 AAAATGCAATGACAAT
1 AAAATGCAATGACAAT
64293431 GTAAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:64304826 original size:17 final size:17
Alignment explanation
Indices: 64304765--64304830 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
64304755 TTCATGCATA
* * *
64304765 ATAATAGTTCACTCTAT
1 ATAATAATTCATTCAAT
*
64304782 ATAA-AAGTTCATACAAT
1 ATAATAA-TTCATTCAAT
* * *
64304799 GTAACAGTTCATTCAAT
1 ATAATAATTCATTCAAT
64304816 ATAATAATTCATTCA
1 ATAATAATTCATTCA
64304831 TACAACATCG
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
16 1 0.03
17 35 0.95
18 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAATAATTCATTCAAT
Found at i:64305483 original size:18 final size:18
Alignment explanation
Indices: 64305460--64305499 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
64305450 CTCACAATAC
64305460 ACAGTTTGACAAATTAAT
1 ACAGTTTGACAAATTAAT
* *
64305478 ACAGTTTGCCATATTAAT
1 ACAGTTTGACAAATTAAT
64305496 ACAG
1 ACAG
64305500 ATCACCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (18 bp):
ACAGTTTGACAAATTAAT
Found at i:64305511 original size:18 final size:18
Alignment explanation
Indices: 64305469--64305512 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
64305459 CACAGTTTGA
* **
64305469 CAAATTAATACAGTTTGC
1 CAAATTAATACAGATCAC
*
64305487 CATATTAATACAGATCAC
1 CAAATTAATACAGATCAC
64305505 CAAATTAA
1 CAAATTAA
64305513 CACAATTTGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (18 bp):
CAAATTAATACAGATCAC
Found at i:64309163 original size:42 final size:42
Alignment explanation
Indices: 64309103--64309182 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
64309093 TTTTAGAAAT
* *
64309103 AAACGCCTCTAAAGGTCATGACTTTTAGCCGCGCTTTTATAA
1 AAACGCCTCTAAAAGTCATGACCTTTAGCCGCGCTTTTATAA
*
64309145 AAACGCCGT-TAAAAGTCATGACCTTTAGCGGCGCTTTT
1 AAACGCC-TCTAAAAGTCATGACCTTTAGCCGCGCTTTT
64309183 TCCACAAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (42 bp):
AAACGCCTCTAAAAGTCATGACCTTTAGCCGCGCTTTTATAA
Found at i:64309211 original size:43 final size:43
Alignment explanation
Indices: 64309103--64309257 Score: 154
Period size: 43 Copynumber: 3.6 Consensus size: 43
64309093 TTTTAGAAAT
* * * * *
64309103 AAACGCCTCTAAAGGTCATGACTTTTAGCCGCGCTTTTAT--AA
1 AAACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTT-TCCAC
* * *
64309145 AAACGCCGTTAAAAGTCATGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTTCCAC
* * * *
64309188 AAACGCCGCTAAAGGCCAGGACCTTTCGCGGTGC-TTTTCACGC
1 AAACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTTC-CAC
*
64309231 AAACGCCGCTAAAGGCCAAGACCTTTA
1 AAACGCCGCTAAAGGCCATGACCTTTA
64309258 AAAAATTTAA
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.01
42 38 0.40
43 56 0.59
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTTCCAC
Found at i:64311848 original size:11 final size:11
Alignment explanation
Indices: 64311832--64311857 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
64311822 ATTGTAGAAC
64311832 AAAACAAAAAG
1 AAAACAAAAAG
64311843 AAAACAAAAAG
1 AAAACAAAAAG
64311854 AAAA
1 AAAA
64311858 ATGAGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAG
Found at i:64313061 original size:7 final size:7
Alignment explanation
Indices: 64313051--64313106 Score: 67
Period size: 7 Copynumber: 8.0 Consensus size: 7
64313041 CTCTTAATCT
*
64313051 CTAACCT
1 CTAACCC
64313058 CTAACCC
1 CTAACCC
64313065 CTAACCC
1 CTAACCC
*
64313072 CAAACCC
1 CTAACCC
64313079 CTAACCC
1 CTAACCC
*
64313086 TTAACCC
1 CTAACCC
*
64313093 TTAACCC
1 CTAACCC
*
64313100 TTAACCC
1 CTAACCC
64313107 TTAAACATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.30, C:0.50, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAACCC
Found at i:64313107 original size:7 final size:7
Alignment explanation
Indices: 64313059--64313110 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
64313049 CTCTAACCTC
*
64313059 TAACCCC
1 TAACCCT
*
64313066 TAACCCC
1 TAACCCT
* *
64313073 AAACCCC
1 TAACCCT
64313080 TAACCCT
1 TAACCCT
64313087 TAACCCT
1 TAACCCT
64313094 TAACCCT
1 TAACCCT
64313101 TAACCCT
1 TAACCCT
64313108 TAA
1 TAA
64313111 ACATTATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (7 bp):
TAACCCT
Found at i:64313110 original size:14 final size:14
Alignment explanation
Indices: 64313037--64313106 Score: 70
Period size: 14 Copynumber: 5.0 Consensus size: 14
64313027 CCTTAAATCA
* * *
64313037 CTAACTCTTAATCT
1 CTAACCCTTAACCC
64313051 CTAA-CCTCTAACCC
1 CTAACCCT-TAACCC
**
64313065 CTAACCCCAAACCC
1 CTAACCCTTAACCC
64313079 CTAACCCTTAACCC
1 CTAACCCTTAACCC
*
64313093 TTAACCCTTAACCC
1 CTAACCCTTAACCC
64313107 TTAAACATTA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
13 2 0.04
14 42 0.91
15 2 0.04
ACGTcount: A:0.30, C:0.46, G:0.00, T:0.24
Consensus pattern (14 bp):
CTAACCCTTAACCC
Found at i:64313785 original size:41 final size:41
Alignment explanation
Indices: 64313695--64313886 Score: 246
Period size: 41 Copynumber: 4.7 Consensus size: 41
64313685 AAATTTTTTT
* *
64313695 GCGGCGCTTTTTCAAAAATGCCGC-AAATCTC-GAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
* * *
64313734 GCGGCTCTTTTCCAAAATA-GCCGCTAAAGCTCTGAGCGTTA
1 GCGGCGCTTTTTCAAAA-ACGCCGCTAAAGCTCTGAGCATTA
* *
64313775 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCTCTAAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
* * *
64313816 GCAGCACTTTTTCAAAAATGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
* *
64313857 GCGGTGCTTTTTCAAAAACGTCGCTAAAGC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGC
64313887 CTCGAAAGGT
Statistics
Matches: 132, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
39 20 0.15
40 8 0.06
41 104 0.79
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
Found at i:64313972 original size:39 final size:39
Alignment explanation
Indices: 64313923--64314018 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 39
64313913 TGGGCTTAGG
* *
64313923 TTTTTTGCGGCGCTTTTCTA-AACAACACCGCTAATGCT-A
1 TTTTTAGCGGCGTTTTTC-AGAA-AACACCGCTAATGCTCA
* *
64313962 TTTTTAGCGGCGTTTTTCAGAAAGCACCGCTAATTCTCGA
1 TTTTTAGCGGCGTTTTTCAGAAAACACCGCTAATGCTC-A
*
64314002 TCTTTAGCGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
64314019 TATCCAAACG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
38 14 0.29
39 18 0.37
40 17 0.35
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.39
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTCAGAAAACACCGCTAATGCTCA
Found at i:64316267 original size:20 final size:20
Alignment explanation
Indices: 64316223--64316349 Score: 69
Period size: 21 Copynumber: 6.2 Consensus size: 20
64316213 CTTTTATGGC
* * *
64316223 GCATTTTGTTAGCCTTTTTT
1 GCATTTTATTAGCCTTTGTG
*
64316243 TCATTTTATTAGCCTTTGTG
1 GCATTTTATTAGCCTTTGTG
**
64316263 GCATTTT-GGACGACCTTTGTG
1 GCATTTTATTA-G-CCTTTGTG
* *
64316284 GCATTCTATTAACCTTTTGTG
1 GCATTTTATTAGCC-TTTGTG
* * * *
64316305 ACATTTTGATATGGCTTTTATG
1 GCATTTT-AT-TAGCCTTTGTG
* *
64316327 GCATTCTATTA-ACTTTGTG
1 GCATTTTATTAGCCTTTGTG
64316346 GCAT
1 GCAT
64316350 ACTCTGTATA
Statistics
Matches: 78, Mismatches: 23, Indels: 13
0.68 0.20 0.11
Matches are distributed among these distances:
19 10 0.13
20 26 0.33
21 27 0.35
22 13 0.17
23 2 0.03
ACGTcount: A:0.17, C:0.16, G:0.18, T:0.49
Consensus pattern (20 bp):
GCATTTTATTAGCCTTTGTG
Found at i:64316294 original size:41 final size:41
Alignment explanation
Indices: 64316244--64316349 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 41
64316234 GCCTTTTTTT
* *
64316244 CATTTTATTAGCCTTTGTGGCATTTTG-GACGACCTTTGTGG
1 CATTCTATTA-CCTTTGTGGCATTTTGAGACGACCTTTATGG
* * * * *
64316285 CATTCTATTAACCTTTTGTGACATTTTGATATGGCTTTTATGG
1 CATTCTATT-ACC-TTTGTGGCATTTTGAGACGACCTTTATGG
*
64316328 CATTCTATTAACTTTGTGGCAT
1 CATTCTATTACCTTTGTGGCAT
64316350 ACTCTGTATA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
41 19 0.36
42 16 0.30
43 18 0.34
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.46
Consensus pattern (41 bp):
CATTCTATTACCTTTGTGGCATTTTGAGACGACCTTTATGG
Found at i:64316302 original size:21 final size:20
Alignment explanation
Indices: 64316278--64316349 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 20
64316268 TTGGACGACC
64316278 TTTGTGGCATTCTATTAACCT
1 TTTGTGGCATTCTATTAA-CT
* * **
64316299 TTTGTGACATTTTGATATGGCT
1 TTTGTGGCATTCT-AT-TAACT
*
64316321 TTTATGGCATTCTATTAAC-
1 TTTGTGGCATTCTATTAACT
64316340 TTTGTGGCAT
1 TTTGTGGCAT
64316350 ACTCTGTATA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
19 9 0.23
20 2 0.05
21 13 0.33
22 14 0.36
23 1 0.03
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (20 bp):
TTTGTGGCATTCTATTAACT
Found at i:64319670 original size:19 final size:20
Alignment explanation
Indices: 64319643--64319685 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
64319633 CATTTTATAA
*
64319643 ATAAAATAT-TATCACTTTT
1 ATAAAATATAAATCACTTTT
* *
64319662 ATAACATATAAATCATTTTT
1 ATAAAATATAAATCACTTTT
64319682 ATAA
1 ATAA
64319686 TAAACTCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAAATATAAATCACTTTT
Found at i:64332417 original size:15 final size:17
Alignment explanation
Indices: 64332394--64332433 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
64332384 TTTTTATGTT
64332394 TTATAT-ATATTATTTTA
1 TTATATAATA-TATTTTA
*
64332411 TTATATAATATATTATA
1 TTATATAATATATTTTA
64332428 TTATAT
1 TTATAT
64332434 TGTATTGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATATAATATATTTTA
Found at i:64332433 original size:5 final size:5
Alignment explanation
Indices: 64332394--64332458 Score: 64
Period size: 5 Copynumber: 13.2 Consensus size: 5
64332384 TTTTTATGTT
* *
64332394 TTATA -TATA TTAT- TT-TA TTATA TAATATA TTATA TTATA TTGTA TTGTA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
*
64332443 TTGTA TTATA TTATA T
1 TTATA TTATA TTATA T
64332459 AAATTAAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
3 1 0.02
4 8 0.15
5 39 0.74
7 5 0.09
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:64333376 original size:24 final size:23
Alignment explanation
Indices: 64333335--64333381 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
64333325 TACTCATGGG
64333335 ACATTTAAAGTAAGGTAAGTAATA
1 ACATTTAAAGTAAGGTAAG-AATA
*
64333359 ACATTTGAAATTAA-GTAAGAATA
1 ACATTT-AAAGTAAGGTAAGAATA
64333382 TGTGTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (23 bp):
ACATTTAAAGTAAGGTAAGAATA
Found at i:64334981 original size:14 final size:14
Alignment explanation
Indices: 64334944--64334989 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
64334934 CCAAGCTGGA
64334944 AAGGACCTTATGTGG
1 AAGG-CCTTATGTGG
*
64334959 AAGACCCTTATGTGG
1 AAG-GCCTTATGTGG
*
64334974 AAGGCCTTATTTGG
1 AAGGCCTTATGTGG
64334988 AA
1 AA
64334990 AAGCGTCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (14 bp):
AAGGCCTTATGTGG
Found at i:64336509 original size:44 final size:44
Alignment explanation
Indices: 64336461--64336694 Score: 132
Period size: 44 Copynumber: 5.3 Consensus size: 44
64336451 AGACACTAGC
**
64336461 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGCATTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* ** * * * * * * *
64336505 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAG-C
1 CTTGCCTCCCTGCATTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
* ** * * *
64336549 CTTGCCTCCCAGGTTTGGAGTGGAGCAGGTTAAAAATTGCAGAT
1 CTTGCCTCCCTGCATTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* ** * * ** * * * *
64336593 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAG-C
1 CTTGCCTCCCTGCATTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
* *
64336637 CTTGCCTCCCTG-AGTTGTAGCGGAGTAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGCA-TTGCAGCGGAGCAGGTTAAAAATAGCAGAT
*
64336681 CTTGCCTTCCTGCA
1 CTTGCCTCCCTGCA
64336695 CCGAAGGTGA
Statistics
Matches: 125, Mismatches: 59, Indels: 11
0.64 0.30 0.06
Matches are distributed among these distances:
43 33 0.26
44 57 0.46
45 35 0.28
ACGTcount: A:0.26, C:0.27, G:0.25, T:0.22
Consensus pattern (44 bp):
CTTGCCTCCCTGCATTGCAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:64336736 original size:88 final size:88
Alignment explanation
Indices: 64336315--64336725 Score: 599
Period size: 88 Copynumber: 4.7 Consensus size: 88
64336305 AGCAGATCAG
* * * * *
64336315 TAAAGATAACAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAACCTTGCTT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
64336380 CCCTGGGTTGTAGCGGAGCAGGT
66 CCCTGGGTTGTAGCGGAGCAGGT
* * * * *
64336403 TAAAAATAGTAGATCTTGCCCTCCTACACCGACAGCAAAGCAGATCGAAGACACTAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
64336468 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGTAGCGGAGCAGGT
*
64336491 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * * *
64336556 CCCAGGTTTGGAGTGGAGCAGGT
66 CCCTGGGTTGTAGCGGAGCAGGT
*
64336579 TAAAAATTGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
64336644 CCCTGAGTTGTAGCGGAGTAGGT
66 CCCTGGGTTGTAGCGGAGCAGGT
* * * *
64336667 TAAAAATAGCAGATCTTGCCTTCCTGCACCGA-AGGTGAAGCAAATCGATGACCCCAGCC
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACA-GCGAAGCAGATCGAAGACACCAGCC
64336726 CTATCTCCCT
Statistics
Matches: 288, Mismatches: 34, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
87 1 0.00
88 287 1.00
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.20
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGTAGCGGAGCAGGT
Found at i:64336793 original size:44 final size:43
Alignment explanation
Indices: 64336725--64336846 Score: 147
Period size: 44 Copynumber: 2.8 Consensus size: 43
64336715 TGACCCCAGC
*
64336725 CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAATATTGT-AAGT
1 CCTATCTCCCTGG-CAGCAGTGGAATAGGTTGAAGATTGTGAA-T
* * *
64336769 TCTATCTCCCTGGTCAGCATTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGG-CAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
64336813 CCTATCTCCCTGAGCAACAGTGGAGTAGGTTGAA
1 CCTATCTCCCTG-GCAGCAGTGGAATAGGTTGAA
64336847 AATAGCAGAT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
44 63 0.95
45 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (43 bp):
CCTATCTCCCTGGCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:64336970 original size:50 final size:50
Alignment explanation
Indices: 64336916--64337014 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
64336906 CGCCTTGACG
* *
64336916 TTGCAATGGAAAAGATTGAAGCCACAACGGCGAATCTTATTTCCCTGGCA
1 TTGCAACGGAAAAGATTGAAGCCACAACGGCGAATCTTATCTCCCTGGCA
* ** * *
64336966 TTGCAGCGGAGTAGATTGAAGCCACGACGGTGAATCTTATCTCCCTGGC
1 TTGCAACGGAAAAGATTGAAGCCACAACGGCGAATCTTATCTCCCTGGC
64337015 GTTAAGGCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.24
Consensus pattern (50 bp):
TTGCAACGGAAAAGATTGAAGCCACAACGGCGAATCTTATCTCCCTGGCA
Found at i:64337265 original size:44 final size:44
Alignment explanation
Indices: 64337210--64337672 Score: 244
Period size: 44 Copynumber: 10.7 Consensus size: 44
64337200 GAAGATGATG
* *
64337210 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAAC
* * * * *
64337254 AATCCTATCTCCCTAAAGTCGCAGTGGAGCGGATTAAA-ATCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAAC
* * * *** **
64337297 AGATCTTATCTCTCTGAAATTGCAG-AGAGCAGATCGCATCT-A-
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAAC
* **
64337339 GA-CTTATCTCCCTGAAGTTGCAGTGGAGCAGGCT-AAG-TAAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAA-C
* * * * **
64337381 AAGCCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGC
1 AA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAGATAAC
* ** *
64337426 GAATCTTATCTCCCTGAAGTTGCAGTTGAGCAGATTAAAGCCAAT
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAAC
* * ** *
64337471 AATCATATCTCTCTGAAGTTGCAGTGGAGTGGATTAAA-ATCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAAC
* * *
64337514 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCAT--C
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-ATAAC
** * *
64337554 GGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGA-AATC
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAA-C
* * * * *
64337599 AAGTCTTATCCCCCTAAAATTGCAGTGCG-GCAGACTAAATA-AAC
1 AA-TCTTATCTCCCTGAAGTTGCAGTG-GAGCAGATTAAAGATAAC
* * *
64337643 AAATCTCATCTCCCTAAAGTTGTAGTGGAG
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAG
64337673 TGGATTAGAA
Statistics
Matches: 318, Mismatches: 71, Indels: 60
0.71 0.16 0.13
Matches are distributed among these distances:
39 1 0.00
40 43 0.14
41 14 0.04
42 5 0.02
43 24 0.08
44 156 0.49
45 68 0.21
46 7 0.02
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAAC
Found at i:64337459 original size:45 final size:44
Alignment explanation
Indices: 64337341--64337459 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 44
64337331 CGCATCTAGA
* *
64337341 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGCAAGC
1 CTTATCTCCCTGAAGTTGCAGTTGAGCAGACTAAGTAAGCAAGC
* * *
64337385 CTTATC-CTCCTGAAGTTGTAG-TGAGGCAGACTGAAG-ATGGCGAA-T
1 CTTATCTC-CCTGAAGTTGCAGTTGA-GCAGACT-AAGTA-AGC-AAGC
64337430 CTTATCTCCCTGAAGTTGCAGTTGAGCAGA
1 CTTATCTCCCTGAAGTTGCAGTTGAGCAGA
64337460 TTAAAGCCAA
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
43 3 0.05
44 25 0.40
45 28 0.45
46 6 0.10
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTTGAGCAGACTAAGTAAGCAAGC
Found at i:64337570 original size:217 final size:218
Alignment explanation
Indices: 64337195--64337672 Score: 683
Period size: 217 Copynumber: 2.2 Consensus size: 218
64337185 GCAATTTAAA
* * *
64337195 AGACTGAAGATGATGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAATAATCCT
1 AGACTGAAGATGACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCAT
64337260 ATCTCCCTAAAGTCGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAATTGCAGAGA
66 ATCTCCCTAAAGTCGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAATTGCAGAGA
* * *
64337325 GCAGATCGCATCTAGACTTATCTCCCTGAAGTTGCAGTGGAGCAGGCT-AAGTAAGCAAGCCTTA
131 GCAGATCGCATCGAGACTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGCCTTA
* * * *
64337389 TCCTCCTGAAGTTGTAGTGAGGC
196 TCCCCCTAAAATTGCAGTGAGGC
* *
64337412 AGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTTGAGCAGATTAAAGCCAATAATCAT
1 AGACTGAAGATGACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCAT
* * * * *
64337477 ATCTCTCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGA
66 ATCTCCCTAAAGTCGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAATTGCAGAGA
* * * *
64337542 GCAGATCGCATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCAAGTCTTA
131 GCAGATCGCATCGAGACTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGCCTTA
*
64337607 TCCCCCTAAAATTGCAGTGCGGC
196 TCCCCCTAAAATTGCAGTGAGGC
* * * * *
64337630 AGACT-AA-ATAAACAAATCTCATCTCCCTAAAGTTGTAGTGGAG
1 AGACTGAAGAT-GACGAATCTTATCTCCCTGAAGTTGCAGTGGAG
64337673 TGGATTAGAA
Statistics
Matches: 230, Mismatches: 29, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
216 2 0.01
217 192 0.83
218 36 0.16
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (218 bp):
AGACTGAAGATGACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCAT
ATCTCCCTAAAGTCGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAATTGCAGAGA
GCAGATCGCATCGAGACTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGCCTTA
TCCCCCTAAAATTGCAGTGAGGC
Found at i:64338207 original size:19 final size:19
Alignment explanation
Indices: 64338183--64338255 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
64338173 AATCTTCAAG
64338183 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
64338202 GATATGCAGTCTTAGATAT
1 GATATGCAATCTTAGATAT
*
64338221 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
64338240 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
64338256 AGTTATAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:64338722 original size:3 final size:3
Alignment explanation
Indices: 64338714--64338754 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
64338704 ATCTTGTATC
64338714 ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT AT
64338755 ATTCATGCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:64338975 original size:2 final size:2
Alignment explanation
Indices: 64338963--64339001 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
64338953 TTTCTAATGA
*
64338963 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64339002 CACGAACATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:64344253 original size:15 final size:14
Alignment explanation
Indices: 64344226--64344253 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
64344216 AATTAGTGTT
64344226 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
64344240 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
64344254 TGGGGGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
GAAAACTAAAAAAA
Found at i:64345086 original size:41 final size:41
Alignment explanation
Indices: 64344976--64345113 Score: 143
Period size: 42 Copynumber: 3.4 Consensus size: 41
64344966 GATGCTAACG
* * * * * * *
64344976 GAAAAACGCTACGATAGGTAAAGCAGTAGCGGGGTTTATGA
1 GAAAAACGCCACAAAAGGTCAAGCATTAGCGGCGTTTATAA
* **
64345017 GAAAAACAACTGCAAAAGGTCAAGCATTAGCGGCGTTTATAA
1 GAAAAAC-GCCACAAAAGGTCAAGCATTAGCGGCGTTTATAA
* *
64345059 GAAAAACGCCACAAAAGGTCAAGCATTAGCAGCG-CTATAA
1 GAAAAACGCCACAAAAGGTCAAGCATTAGCGGCGTTTATAA
*
64345099 GAAAAACGCCGCAAA
1 GAAAAACGCCACAAA
64345114 GTATCATTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
40 19 0.23
41 30 0.37
42 33 0.40
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (41 bp):
GAAAAACGCCACAAAAGGTCAAGCATTAGCGGCGTTTATAA
Found at i:64345170 original size:19 final size:19
Alignment explanation
Indices: 64345146--64345184 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
64345136 ACGGCATCTT
64345146 TTTGCTCTGCTCAGTTTTA
1 TTTGCTCTGCTCAGTTTTA
64345165 TTTGCTCTGCTCAGTTTTA
1 TTTGCTCTGCTCAGTTTTA
64345184 T
1 T
64345185 CCCCAACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.21, G:0.15, T:0.54
Consensus pattern (19 bp):
TTTGCTCTGCTCAGTTTTA
Found at i:64347571 original size:41 final size:39
Alignment explanation
Indices: 64347526--64347653 Score: 114
Period size: 39 Copynumber: 3.2 Consensus size: 39
64347516 AGCGGTATTT
**
64347526 TTAGCGGCG-TTTGGACAAAAAACGCCGCTAAAAATTGAGCA
1 TTAGCGGCGCTTT-GA-AAAAAACGCCGCT-AAAATACAGCA
* **
64347567 TTAGCGGCGCTTTTAGGAAAACGCCGCTAAAATACAGCA
1 TTAGCGGCGCTTTGAAAAAAACGCCGCTAAAATACAGCA
* *** * * *
64347606 TTAGCGGCACTTTTTGAAAAATGCTGCTAAAATAGAGCA
1 TTAGCGGCGCTTTGAAAAAAACGCCGCTAAAATACAGCA
64347645 TTAGCGGCG
1 TTAGCGGCG
64347654 TTTTCCAAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
39 50 0.68
40 11 0.15
41 10 0.14
42 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (39 bp):
TTAGCGGCGCTTTGAAAAAAACGCCGCTAAAATACAGCA
Found at i:64347610 original size:39 final size:39
Alignment explanation
Indices: 64347543--64347657 Score: 151
Period size: 39 Copynumber: 2.9 Consensus size: 39
64347533 CGTTTGGACA
*
64347543 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTTAG
1 AAAAACGCCGCT-AAAATAGAGCATTAGCGGCGCTTTTAG
* * * *
64347583 GAAAACGCCGCTAAAATACAGCATTAGCGGCACTTTTTG
1 AAAAACGCCGCTAAAATAGAGCATTAGCGGCGCTTTTAG
* *
64347622 AAAAATGCTGCTAAAATAGAGCATTAGCGGCG-TTTT
1 AAAAACGCCGCTAAAATAGAGCATTAGCGGCGCTTTT
64347658 CCAAGAAGCG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 4 0.06
39 50 0.77
40 11 0.17
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (39 bp):
AAAAACGCCGCTAAAATAGAGCATTAGCGGCGCTTTTAG
Found at i:64347902 original size:41 final size:41
Alignment explanation
Indices: 64347716--64347915 Score: 137
Period size: 41 Copynumber: 4.9 Consensus size: 41
64347706 CTTTTGAGGA
*
64347716 TTTAGCGGCG-TTTT-AAAAATGCG-TCGCTAATGAT-TGGGCC
1 TTTAGCGGCGTTTTTCAAAAA-GCGCT-GCTAATGCTCTGGG-C
** *
64347756 TTTAGCGATGTTTTTCAAAAAGCG-T-CAAGAATGCT-TGGGGC
1 TTTAGCGGCGTTTTTCAAAAAGCGCTGC--TAATGCTCT-GGGC
* * * * *
64347797 TTTAGCGGCATTTTACAAAAAACGCCGCGAATGCTC-GGGAC
1 TTTAGCGGCGTTTTTCAAAAAGCGCTGCTAATGCTCTGGG-C
* ** *
64347838 TTAAGCGGCGTTTCCCAATAAGCGCTGCTAATGCTCTGGGC
1 TTTAGCGGCGTTTTTCAAAAAGCGCTGCTAATGCTCTGGGC
* **
64347879 TTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCT
1 TTTAGCGGCGTTTTTCAAAAAGCGCTGCTAATGCTCT
64347916 ATTTTTAGCG
Statistics
Matches: 125, Mismatches: 25, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
39 1 0.01
40 11 0.09
41 101 0.81
42 11 0.09
43 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTCAAAAAGCGCTGCTAATGCTCTGGGC
Found at i:64348274 original size:14 final size:14
Alignment explanation
Indices: 64348255--64348459 Score: 105
Period size: 14 Copynumber: 13.9 Consensus size: 14
64348245 TATCACTATA
*
64348255 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
64348269 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* *
64348283 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
*
64348297 GTTTAGGTGTTACCAT-
1 GTTTAGG-GTT--TATG
*
64348313 -TTTAAGGTTTATG
1 GTTTAGGGTTTATG
*
64348326 GATTATGGGTTTATAG
1 GTTTA-GGGTTTAT-G
*
64348342 G-TTATGGTTTATG
1 GTTTAGGGTTTATG
*
64348355 GTTTATGGTTTATG
1 GTTTAGGGTTTATG
*
64348369 GTTTAAAGGCTGGTATTTAAG
1 GTTT--A-G--GG--TTTATG
64348390 GTTTAGAGG-TTATG
1 GTTTAG-GGTTTATG
* *
64348404 TGTTAAGGGTTTAGG
1 -GTTTAGGGTTTATG
*
64348419 GTTTTAGGGTTTTAAG
1 G-TTTAGGG-TTTATG
64348435 GTTTA-GGTTTATG
1 GTTTAGGGTTTATG
*
64348448 GTTTAGGATTTA
1 GTTTAGGGTTTA
64348460 GATTAACTAG
Statistics
Matches: 148, Mismatches: 23, Indels: 40
0.70 0.11 0.19
Matches are distributed among these distances:
12 2 0.01
13 12 0.08
14 72 0.49
15 37 0.25
16 9 0.06
17 3 0.02
18 1 0.01
19 3 0.02
21 9 0.06
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.47
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:64348300 original size:7 final size:7
Alignment explanation
Indices: 64348255--64348373 Score: 82
Period size: 7 Copynumber: 16.7 Consensus size: 7
64348245 TATCACTATA
*
64348255 GTTTAGG
1 GTTTATG
*
64348262 GTTTTTG
1 GTTTATG
*
64348269 GTTTAGG
1 GTTTATG
*
64348276 GTATATG
1 GTTTATG
64348283 GTTTA-G
1 GTTTATG
*
64348289 AGTTTAAG
1 -GTTTATG
64348297 GTTTA-G
1 GTTTATG
**
64348303 GTGTTACCA
1 GT-TTA-TG
* *
64348312 TTTTAAG
1 GTTTATG
64348319 GTTTATG
1 GTTTATG
*
64348326 GATTATGG
1 GTTTAT-G
64348334 GTTTATAG
1 GTTTAT-G
64348342 G-TTATG
1 GTTTATG
64348348 GTTTATG
1 GTTTATG
64348355 GTTTATG
1 GTTTATG
64348362 GTTTATG
1 GTTTATG
64348369 GTTTA
1 GTTTA
64348374 AAGGCTGGTA
Statistics
Matches: 89, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
6 6 0.07
7 70 0.79
8 12 0.13
9 1 0.01
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (7 bp):
GTTTATG
Found at i:64348350 original size:29 final size:27
Alignment explanation
Indices: 64348318--64348371 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
64348308 ACCATTTTAA
64348318 GGTTTATGGATTATGGGTTTATAGGTTAT
1 GGTTTATGGATTAT-GGTTTAT-GGTTAT
*
64348347 GGTTTATGGTTTATGGTTTATGGTT
1 GGTTTATGGATTATGGTTTATGGTT
64348372 TAAAGGCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.17
28 7 0.29
29 13 0.54
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (27 bp):
GGTTTATGGATTATGGTTTATGGTTAT
Found at i:64348419 original size:7 final size:7
Alignment explanation
Indices: 64348409--64348460 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
64348399 TTATGTGTTA
64348409 AGGGTTT
1 AGGGTTT
64348416 AGGGTTTT
1 AGGG-TTT
64348424 AGGGTTTT
1 AGGG-TTT
*
64348432 AAGGTTT
1 AGGGTTT
64348439 A-GGTTT
1 AGGGTTT
*
64348445 ATGGTTT
1 AGGGTTT
*
64348452 AGGATTT
1 AGGGTTT
64348459 AG
1 AG
64348461 ATTAACTAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
6 6 0.15
7 20 0.50
8 14 0.35
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
AGGGTTT
Found at i:64348429 original size:15 final size:14
Alignment explanation
Indices: 64348409--64348460 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
64348399 TTATGTGTTA
64348409 AGGGTTTAGGGTTTT
1 AGGGTTTAGGG-TTT
*
64348424 AGGGTTTTAAGGTTT
1 AGGG-TTTAGGGTTT
*
64348439 A-GGTTTATGGTTT
1 AGGGTTTAGGGTTT
*
64348452 AGGATTTAG
1 AGGGTTTAG
64348461 ATTAACTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 10 0.32
14 7 0.23
15 8 0.26
16 6 0.19
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (14 bp):
AGGGTTTAGGGTTT
Found at i:64348526 original size:7 final size:7
Alignment explanation
Indices: 64348505--64348672 Score: 52
Period size: 7 Copynumber: 23.7 Consensus size: 7
64348495 TTAATTATCA
*
64348505 TTATAGT
1 TTATGGT
*
64348512 TTAGGGT
1 TTATGGT
64348519 TTATGGT
1 TTATGGT
*
64348526 TTAAGGT
1 TTATGGT
*
64348533 ATATGGT
1 TTATGGT
*
64348540 TTAGGGT
1 TTATGGT
*
64348547 TTAAGGT
1 TTATGGT
*
64348554 TTA-GGAG
1 TTATGG-T
***
64348561 TTACTACC
1 TTA-TGGT
*
64348569 TTAAGGT
1 TTATGGT
*
64348576 TTATGGA
1 TTATGGT
*
64348583 TTATGGA
1 TTATGGT
*
64348590 TTATGGA
1 TTATGGT
64348597 TTATGGTT
1 TTATGG-T
* *
64348605 TTAAGGG
1 TTATGGT
*
64348612 TTAGGGT
1 TTATGGT
*
64348619 TTAAGG-
1 TTATGGT
*
64348625 TTATGGG
1 TTATGGT
*
64348632 TTAGGGGT
1 TTA-TGGT
* *
64348640 TAAGGGT
1 TTATGGT
* *
64348647 TAAGGGT
1 TTATGGT
*
64348654 TTATAGT
1 TTATGGT
*
64348661 TTATGTT
1 TTATGGT
64348668 TTATG
1 TTATG
64348673 ATTTTGGGTT
Statistics
Matches: 121, Mismatches: 34, Indels: 12
0.72 0.20 0.07
Matches are distributed among these distances:
6 7 0.06
7 102 0.84
8 12 0.10
ACGTcount: A:0.23, C:0.02, G:0.31, T:0.44
Consensus pattern (7 bp):
TTATGGT
Found at i:64348527 original size:14 final size:14
Alignment explanation
Indices: 64348505--64348558 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
64348495 TTAATTATCA
*
64348505 TTATAGTTTAGGGT
1 TTATGGTTTAGGGT
*
64348519 TTATGGTTTAAGGT
1 TTATGGTTTAGGGT
*
64348533 ATATGGTTTAGGGT
1 TTATGGTTTAGGGT
*
64348547 TTAAGGTTTAGG
1 TTATGGTTTAGG
64348559 AGTTACTACC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
TTATGGTTTAGGGT
Found at i:64348630 original size:35 final size:36
Alignment explanation
Indices: 64348590--64348665 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 36
64348580 GGATTATGGA
**
64348590 TTATGGATTATGGTTTTAAGGGTT-AGGGTTTA-AGG
1 TTATGGATTA-GGGGTTAAGGGTTAAGGGTTTATAGG
* *
64348625 TTATGGGTTAGGGGTTAAGGGTTAAGGGTTTATAGT
1 TTATGGATTAGGGGTTAAGGGTTAAGGGTTTATAGG
64348661 TTATG
1 TTATG
64348666 TTTTATGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 11 0.31
35 17 0.49
36 7 0.20
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.42
Consensus pattern (36 bp):
TTATGGATTAGGGGTTAAGGGTTAAGGGTTTATAGG
Found at i:64348634 original size:20 final size:21
Alignment explanation
Indices: 64348605--64348654 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
64348595 GATTATGGTT
*
64348605 TTAAGGGTTAGGGTTTAA-GG
1 TTAAGGGTTAGGGGTTAAGGG
*
64348625 TTATGGGTTAGGGGTTAAGGG
1 TTAAGGGTTAGGGGTTAAGGG
64348646 TTAAGGGTT
1 TTAAGGGTT
64348655 TATAGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (21 bp):
TTAAGGGTTAGGGGTTAAGGG
Found at i:64353126 original size:43 final size:43
Alignment explanation
Indices: 64353078--64353193 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
64353068 ATAGTGGCGC
* *
64353078 TTGTGGTAGACGCGTCACTAAAGGTCATGATTTTTAGCGGAGT
1 TTGTGGTAGAAGCGTCACTAAAGGTCATGATCTTTAGCGGAGT
*
64353121 TTGTGGTAGAAGCGTCGCTAAAGGTCATGATCTTTAGCGGCA-T
1 TTGTGGTAGAAGCGTCACTAAAGGTCATGATCTTTAGCGG-AGT
* * * * *
64353164 TTGCGGAAGAAGCGCCGCTAAAGGCCATGA
1 TTGTGGTAGAAGCGTCACTAAAGGTCATGA
64353194 GTTAGTGGCG
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 64 0.98
44 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (43 bp):
TTGTGGTAGAAGCGTCACTAAAGGTCATGATCTTTAGCGGAGT
Found at i:64353487 original size:35 final size:35
Alignment explanation
Indices: 64353442--64353508 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
64353432 AAATTTAAAG
*
64353442 ATGATAATCATAACTTATATAAACATTTAAAGTTT
1 ATGATAATCATAACTTACATAAACATTTAAAGTTT
* *
64353477 ATGATTATCATAATTTACATAAACATTTAAAG
1 ATGATAATCATAACTTACATAAACATTTAAAG
64353509 AGTAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (35 bp):
ATGATAATCATAACTTACATAAACATTTAAAGTTT
Found at i:64353583 original size:56 final size:56
Alignment explanation
Indices: 64353519--64353680 Score: 211
Period size: 56 Copynumber: 3.1 Consensus size: 56
64353509 AGTAAAAAAA
** *
64353519 AACTTTGGACCATAACTTATTTAACTTACATAATACATAATTATATATCATATCAT
1 AACTTTGGACCATAACTTACATAACTTACATAATACATAAATATATATCATATCAT
*
64353575 AACTTTGGATCATAACTTACATAACTTACATAATACATAAATATATATCATATCAT
1 AACTTTGGACCATAACTTACATAACTTACATAATACATAAATATATATCATATCAT
64353631 AAC-TT--A-CATAACTTACATAAC-T---T-A-A-ATAAATATATATCATATCAT
1 AACTTTGGACCATAACTTACATAACTTACATAATACATAAATATATATCATATCAT
64353676 AACTT
1 AACTT
64353681 ACATAAAAAT
Statistics
Matches: 101, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
45 23 0.23
46 2 0.02
47 1 0.01
48 1 0.01
51 1 0.01
52 15 0.15
53 1 0.01
55 2 0.02
56 55 0.54
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.37
Consensus pattern (56 bp):
AACTTTGGACCATAACTTACATAACTTACATAATACATAAATATATATCATATCAT
Found at i:64353599 original size:9 final size:9
Alignment explanation
Indices: 64353529--64353686 Score: 78
Period size: 9 Copynumber: 17.6 Consensus size: 9
64353519 AACTTTGGAC
64353529 CATAACTTA
1 CATAACTTA
**
64353538 TTTAACTTA
1 CATAACTTA
64353547 CATAA--TA
1 CATAACTTA
64353554 CATAA-TTA
1 CATAACTTA
* * *
64353562 TATATCATA
1 CATAACTTA
64353571 TCATAACTTTGGA
1 -CATAAC-TT--A
64353584 TCATAACTTA
1 -CATAACTTA
64353594 CATAACTTA
1 CATAACTTA
64353603 CATAA--TA
1 CATAACTTA
*
64353610 CATAA-ATA
1 CATAACTTA
* * *
64353618 TATATCATA
1 CATAACTTA
64353627 TCATAACTTA
1 -CATAACTTA
64353637 CATAACTTA
1 CATAACTTA
64353646 CATAACTTA
1 CATAACTTA
* *
64353655 AATAA-ATA
1 CATAACTTA
* * *
64353663 TATATCATA
1 CATAACTTA
64353672 TCATAACTTA
1 -CATAACTTA
64353682 CATAA
1 CATAA
64353687 AAATTTGGAT
Statistics
Matches: 116, Mismatches: 22, Indels: 22
0.73 0.14 0.14
Matches are distributed among these distances:
7 14 0.12
8 15 0.13
9 59 0.51
10 17 0.15
11 1 0.01
12 2 0.02
13 8 0.07
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (9 bp):
CATAACTTA
Found at i:64353637 original size:43 final size:44
Alignment explanation
Indices: 64353583--64353686 Score: 183
Period size: 45 Copynumber: 2.4 Consensus size: 44
64353573 ATAACTTTGG
*
64353583 ATCATAACTTACATAACTTACATAA-TACATAAATATATATCAT
1 ATCATAACTTACATAACTTACATAACTAAATAAATATATATCAT
64353626 ATCATAACTTACATAACTTACATAACTTAAATAAATATATATCAT
1 ATCATAACTTACATAACTTACATAAC-TAAATAAATATATATCAT
64353671 ATCATAACTTACATAA
1 ATCATAACTTACATAA
64353687 AAATTTGGAT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
43 25 0.43
45 33 0.57
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (44 bp):
ATCATAACTTACATAACTTACATAACTAAATAAATATATATCAT
Found at i:64353677 original size:36 final size:40
Alignment explanation
Indices: 64353583--64353686 Score: 126
Period size: 43 Copynumber: 2.6 Consensus size: 40
64353573 ATAACTTTGG
*
64353583 ATCATAACTTACATAACTTACATAATACATAAATATATATCAT
1 ATCATAAC-TACATAACTTACAT-A-ACATAAATAAATATCAT
*
64353626 ATCATAACTTACATAACTTACATAACTTAAATAAATAT-AT
1 ATCATAAC-TACATAACTTACATAACATAAATAAATATCAT
64353666 ATCAT-A-T-CATAACTTACATAA
1 ATCATAACTACATAACTTACATAA
64353687 AAATTTGGAT
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
36 14 0.24
37 1 0.02
39 1 0.02
40 7 0.12
41 12 0.20
42 1 0.02
43 23 0.39
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (40 bp):
ATCATAACTACATAACTTACATAACATAAATAAATATCAT
Found at i:64359751 original size:43 final size:43
Alignment explanation
Indices: 64359690--64359848 Score: 124
Period size: 43 Copynumber: 3.7 Consensus size: 43
64359680 TTTCCACAAA
* * * *
64359690 CGCCGCCAAAGAACATGACTTTTATCGGCGCTTTTAGTAAAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAGGAAAAG
* * *
64359733 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTGGGGAAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAGGAAAAG
* * ** * *
64359776 CACCGCTAAAGGTA-ATGTTCTTTAGCGGC-ATTTGTAGGGAAAG
1 CGCCGCTAAA-GAACATGACCTTTAGCGGCGCTTT-TAGGAAAAG
* * * **
64359819 CGCAGCCAAAGGACATGTTCTTTAGCGGCG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCG
64359849 TTTGTGTGAG
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
42 5 0.05
43 88 0.93
44 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (43 bp):
CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAGGAAAAG
Found at i:64359853 original size:43 final size:43
Alignment explanation
Indices: 64359729--64359853 Score: 153
Period size: 43 Copynumber: 2.9 Consensus size: 43
64359719 GCTTTTAGTA
* ** * *
64359729 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTGGGG
1 AAAGCGCCGCTAAAGGACATGTTCTTTAGCGGCGTTTGTAGGG
* *
64359772 AAAGCACCGCTAAAGGTA-ATGTTCTTTAGCGGCATTTGTAGGG
1 AAAGCGCCGCTAAAGG-ACATGTTCTTTAGCGGCGTTTGTAGGG
* *
64359815 AAAGCGCAGCCAAAGGACATGTTCTTTAGCGGCGTTTGT
1 AAAGCGCCGCTAAAGGACATGTTCTTTAGCGGCGTTTGT
64359854 GTGAGAAGTG
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 1 0.01
43 67 0.97
44 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGGACATGTTCTTTAGCGGCGTTTGTAGGG
Found at i:64368462 original size:16 final size:18
Alignment explanation
Indices: 64368427--64368464 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
64368417 GATATTAATA
64368427 ATTCATTCCAAATATTTT
1 ATTCATTCCAAATATTTT
*
64368445 ATTCA-TCCAACT-TTTT
1 ATTCATTCCAAATATTTT
64368461 ATTC
1 ATTC
64368465 TCTCCCTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTCATTCCAAATATTTT
Found at i:64373097 original size:19 final size:19
Alignment explanation
Indices: 64373073--64373111 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
64373063 ATGTCAAAAT
64373073 TTTCAAGTATCCAAAT-TGA
1 TTTCAAGTAT-CAAATGTGA
*
64373092 TTTCAATTATCAAATGTGA
1 TTTCAAGTATCAAATGTGA
64373111 T
1 T
64373112 AAATCAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (19 bp):
TTTCAAGTATCAAATGTGA
Found at i:64381201 original size:92 final size:90
Alignment explanation
Indices: 64380914--64381263 Score: 384
Period size: 91 Copynumber: 3.8 Consensus size: 90
64380904 ATAACACATC
* * *
64380914 AGATGCACATAGTGCAAAGCCCGTAGGCTAAAAATTCTCCAC-CAATAACACGCCAGTTAGCTCA
1 AGATGCACATAGTGCAAAGCCCGTAGGCTAAATATT-TCC-CTCAATAACATGCCAGTTTGCTCA
* * *
64380978 TAAAAGCTATTCCAACCGATATCACACT
64 TAAGAGCTATTCCAA-CGATAACACGCT
* * *
64381006 AGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTTCCCCCAATAACACT-TCAGATTGCTCAT
1 AGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTTCCCTCAATAACA-TGCCAGTTTGCTCAT
64381070 AAGAGCTATTCCAACTGATAA-ATCGCT
65 AAGAGCTATTCCAAC-GATAACA-CGCT
** * * *
64381097 AGATGCACATAGTGCAAA-CCAAATAGGCTAAATATTCTCCCTCGATAACATGCCAGTTTTCTCG
1 AGATGCACATAGTGCAAAGCC-CGTAGGCTAAATATT-TCCCTCAATAACATGCCAGTTTGCTCA
* *
64381161 TAAGAGTTATTCCAATCGATAACACGCC
64 TAAGAGCTATTCCAA-CGATAACACGCT
* * * * * *
64381189 AAATACACATAGTACAAAGCTCGTAGGCTAAATATTTCCCTCGATAACATGCCAGTTTACTCATA
1 AGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTTCCCTCAATAACATGCCAGTTTGCTCATA
*
64381254 ATAGCTATTC
66 AGAGCTATTC
64381264 AAACCAATAT
Statistics
Matches: 220, Mismatches: 28, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
90 5 0.02
91 108 0.49
92 104 0.47
93 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (90 bp):
AGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTTCCCTCAATAACATGCCAGTTTGCTCATA
AGAGCTATTCCAACGATAACACGCT
Found at i:64381216 original size:183 final size:183
Alignment explanation
Indices: 64380914--64381263 Score: 436
Period size: 183 Copynumber: 1.9 Consensus size: 183
64380904 ATAACACATC
**
64380914 AGATGCACATAGTGCAAAGCCCGTAGGCTAAAAATTCTCCACCAATAACACGCCAGTTAGCTCAT
1 AGATGCACATAGTGCAAAGCCAATAGGCTAAAAATTCTCCACCAATAACACGCCAGTTAGCTCAT
* * * * *
64380979 AAAAGCTATTCCAACCGATATCACACTAGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTTC
66 AAAAGCTATTCCAACCGATAACACACCAAATACACATAGTACAAAGCCCGTAGGCTAAATATTTC
* *
64381044 CCCCAATAACACT-TCAGATTGCTCATAAGAGCTATTCCAACTGATAAATCGCT
131 CCCCAATAACA-TGCCAGATTACTCATAAGAGCTATTCCAACTGATAAATCGCT
* * * **
64381097 AGATGCACATAGTGCAAA-CCAAATAGGCTAAATATTCTCC-CTCGATAACATGCCAGTTTTCTC
1 AGATGCACATAGTGCAAAGCC-AATAGGCTAAAAATTCTCCAC-CAATAACACGCCAGTTAGCTC
* * * * * *
64381160 GTAAGAGTTATTCCAATCGATAACACGCCAAATACACATAGTACAAAGCTCGTAGGCTAAATATT
64 ATAAAAGCTATTCCAACCGATAACACACCAAATACACATAGTACAAAGCCCGTAGGCTAAATATT
* * * *
64381225 TCCCTCGATAACATGCCAGTTTACTCATAATAGCTATTC
129 TCCCCCAATAACATGCCAGATTACTCATAAGAGCTATTC
64381264 AAACCAATAT
Statistics
Matches: 140, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
182 4 0.03
183 136 0.97
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (183 bp):
AGATGCACATAGTGCAAAGCCAATAGGCTAAAAATTCTCCACCAATAACACGCCAGTTAGCTCAT
AAAAGCTATTCCAACCGATAACACACCAAATACACATAGTACAAAGCCCGTAGGCTAAATATTTC
CCCCAATAACATGCCAGATTACTCATAAGAGCTATTCCAACTGATAAATCGCT
Found at i:64387203 original size:69 final size:71
Alignment explanation
Indices: 64387077--64387208 Score: 182
Period size: 69 Copynumber: 1.9 Consensus size: 71
64387067 GTTCTAGACA
*
64387077 TTGTTTTGATAGTCTGCTGGAAAATGTTATTTTAGTTTGTTAGTGAGTAGAAGATGAAACTGGTG
1 TTGTTTTGATAGTCTGCTGGAAAATGTTATTTTAGTTTGTTAGTCAGTAGAAGATGAAACTGGTG
64387142 TGGCAG
66 TGGCAG
* * *
64387148 TTGTTTTGATTGTCTGCTGG-AACT-TT-TTCTT-GATTTGTTAGTCAGTAGAATATGAAACTGG
1 TTGTTTTGATAGTCTGCTGGAAAATGTTATT-TTAG-TTTGTTAGTCAGTAGAAGATGAAACTGG
64387209 AACTTTATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
68 3 0.05
69 30 0.55
70 3 0.05
71 19 0.35
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (71 bp):
TTGTTTTGATAGTCTGCTGGAAAATGTTATTTTAGTTTGTTAGTCAGTAGAAGATGAAACTGGTG
TGGCAG
Found at i:64391835 original size:92 final size:91
Alignment explanation
Indices: 64391678--64391886 Score: 269
Period size: 92 Copynumber: 2.3 Consensus size: 91
64391668 TTGATTTTAG
* * *
64391678 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATGACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* * *
64391743 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ACTATTTTAAATTATA
*
64391770 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
64391834 TATGTAATAATTACTATTTTAAATTATA
64 TATGTAATAATTACTATTTTAAATTATA
* * * *
64391862 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
64391887 GTTATAATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 70 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTACTATTTTAAATTATA
Found at i:64392015 original size:66 final size:63
Alignment explanation
Indices: 64391940--64392150 Score: 192
Period size: 66 Copynumber: 3.4 Consensus size: 63
64391930 AAATATATTT
64391940 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
64392005 G
63 G
* * * * **
64392006 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
*
64392060 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
64392124 AG
62 AG
*
64392126 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
64392151 AAATTATATA
Statistics
Matches: 113, Mismatches: 15, Indels: 35
0.69 0.09 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.12
55 5 0.04
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 3 0.03
64 4 0.04
65 9 0.08
66 32 0.28
67 5 0.04
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (63 bp):
AATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:64392044 original size:120 final size:120
Alignment explanation
Indices: 64391909--64392194 Score: 488
Period size: 120 Copynumber: 2.4 Consensus size: 120
64391899 TTAAATTATT
* * * *
64391909 TTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-TTTATAG
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-ATTTTACAG
64391971 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
63 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
64392029 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
64392094 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
64392149 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
64392195 TAAATATGAT
Statistics
Matches: 159, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
119 6 0.04
120 151 0.95
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
Found at i:64392062 original size:15 final size:15
Alignment explanation
Indices: 64392027--64392078 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
64392017 TTAAGAATTT
*
64392027 TATTAAATTAT-ATA
1 TATTTAATTATAATA
64392041 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
64392055 TATTTAATAATAAT-
1 TATTTAATTATAATA
64392069 TATGTTAATT
1 TAT-TTAATT
64392079 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:64392177 original size:16 final size:16
Alignment explanation
Indices: 64392156--64392197 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
64392146 TTATTAAATT
*
64392156 ATATATTTTAATTATA
1 ATATATTTTAATAATA
64392172 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
64392187 AT-TATGTTTAA
1 ATATAT-TTTAA
64392198 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:64392182 original size:15 final size:15
Alignment explanation
Indices: 64392147--64392188 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
64392137 TTAAGAATTT
*
64392147 TATTAAATTAT-ATA
1 TATTTAATTATAATA
64392161 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
64392175 TATTTAATAATAAT
1 TATTTAATTATAAT
64392189 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:64392378 original size:19 final size:21
Alignment explanation
Indices: 64392356--64392409 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
64392346 TGTTTAAATA
64392356 TGAT-TAA-AATATTTATTAC
1 TGATATAATAATATTTATTAC
64392375 TGATAATAATAATATTTATTAC
1 TGAT-ATAATAATATTTATTAC
64392397 TGATAATAATAAT
1 TGAT-ATAATAAT
64392410 CTTTTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.12
21 3 0.09
22 25 0.78
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (21 bp):
TGATATAATAATATTTATTAC
Found at i:64392391 original size:22 final size:22
Alignment explanation
Indices: 64392363--64392409 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
64392353 ATATGATTAA
64392363 AATATTTATTACTGATAATAAT
1 AATATTTATTACTGATAATAAT
64392385 AATATTTATTACTGATAATAAT
1 AATATTTATTACTGATAATAAT
64392407 AAT
1 AAT
64392410 CTTTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
AATATTTATTACTGATAATAAT
Found at i:64393211 original size:16 final size:16
Alignment explanation
Indices: 64393184--64393242 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
64393174 ATTTTTATTT
64393184 TTATTT-TTATTTTTC
1 TTATTTCTTATTTTTC
*
64393199 TTATTTCTTATTTCTTT
1 TTATTTCTTATTT-TTC
*
64393216 TTCATTTTCTTTGTTTTTC
1 TT-A-TTTC-TTATTTTTC
64393235 TT-TTTCTT
1 TTATTTCTT
64393243 GACTTTTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
15 8 0.22
16 10 0.28
17 4 0.11
18 1 0.03
19 8 0.22
20 5 0.14
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.78
Consensus pattern (16 bp):
TTATTTCTTATTTTTC
Found at i:64393224 original size:6 final size:6
Alignment explanation
Indices: 64393157--64393197 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
64393147 TTCCTTCTTC
64393157 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
64393198 CTTATTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:64393238 original size:6 final size:6
Alignment explanation
Indices: 64393154--64393242 Score: 74
Period size: 6 Copynumber: 14.8 Consensus size: 6
64393144 ATGTTCCTTC
* * * * * *
64393154 TTCTTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTCTTAT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTT-T
* *
64393203 TTCTTAT TTCTTT TTCATT TTC--T TTGTTT TTCTTT TTCTT
1 TTCTT-T TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTT
64393243 GACTTTTGAT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
4 3 0.04
6 59 0.79
7 13 0.17
ACGTcount: A:0.10, C:0.09, G:0.01, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:64402498 original size:92 final size:91
Alignment explanation
Indices: 64402279--64402584 Score: 405
Period size: 92 Copynumber: 3.3 Consensus size: 91
64402269 CTCCAGATTA
* * ** * *
64402279 CTCATAAGAGTTATTCCCACCAATAACACATCAGATGCACACAGTACAAAGCCTGTAGGCTAAAT
1 CTCATAAGAGCTATTCCAACCAATAACACGCCAGATGCACATAGTACAAAGCCCGTAGGCTAAAT
64402344 ATTCTCCCCGGTAACACGTCAGTTTT
66 ATTCTCCCCGGTAACACGTCAGTTTT
* * *
64402370 CTCATAAGAGCTATTCCAACCAATATCACGCCAGATGCACATAGTACAAAGCCCATAGGATAAAT
1 CTCATAAGAGCTATTCCAACCAATAACACGCCAGATGCACATAGTACAAAGCCCGTAGGCTAAAT
** *
64402435 ATTCTCATTCGGTAACACGTCAGTTTG
66 ATTCTC-CCCGGTAACACGTCAGTTTT
* ** **
64402462 CTCATAAGAGCTATTCCAACCGATAACACGTTAGATGCACATAGTGTAAAGCCCGTAGGCTAAAT
1 CTCATAAGAGCTATTCCAACCAATAACACGCCAGATGCACATAGTACAAAGCCCGTAGGCTAAAT
* *
64402527 ATTCTCCCCCGATAACACGTCATTTTT
66 ATTCT-CCCCGGTAACACGTCAGTTTT
* *
64402554 CTCATAAGAACTATTCCAACCAATATCACGC
1 CTCATAAGAGCTATTCCAACCAATAACACGC
64402585 TAGAACCTCC
Statistics
Matches: 184, Mismatches: 29, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
91 62 0.34
92 121 0.66
93 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (91 bp):
CTCATAAGAGCTATTCCAACCAATAACACGCCAGATGCACATAGTACAAAGCCCGTAGGCTAAAT
ATTCTCCCCGGTAACACGTCAGTTTT
Found at i:64403758 original size:48 final size:52
Alignment explanation
Indices: 64403704--64403804 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 52
64403694 GAAGGCTTGT
* * * *
64403704 ATAATATTTCTCCTG-TAAA-AAAAAA-A-AGATACTAATTAAATTGTTATA
1 ATAATATTTCTCCAGAAAAATAAAAAATATAGAAACTAATTAAAATGTTATA
64403752 ATAATATTTCTCCAGAAAAATAAAAAATATAGAAACTAATTAAAATGTTATA
1 ATAATATTTCTCCAGAAAAATAAAAAATATAGAAACTAATTAAAATGTTATA
64403804 A
1 A
64403805 GTTTTCAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
48 14 0.31
49 3 0.07
50 6 0.13
51 1 0.02
52 21 0.47
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (52 bp):
ATAATATTTCTCCAGAAAAATAAAAAATATAGAAACTAATTAAAATGTTATA
Found at i:64404462 original size:11 final size:11
Alignment explanation
Indices: 64404446--64404478 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
64404436 GAGAGAAGTG
64404446 ATTTATACTTA
1 ATTTATACTTA
64404457 ATTTATACTTA
1 ATTTATACTTA
64404468 A--TATACTTA
1 ATTTATACTTA
64404477 AT
1 AT
64404479 AAAATAAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
11 12 0.57
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTATACTTA
Found at i:64418303 original size:21 final size:23
Alignment explanation
Indices: 64418260--64418306 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
64418250 AAAATTTTCA
64418260 AAAATTGAAAACAAAAATCTTTT
1 AAAATTGAAAACAAAAATCTTTT
64418283 AAAATT-AAAA-AAAAAGT-TTTT
1 AAAATTGAAAACAAAAA-TCTTTT
64418304 AAA
1 AAA
64418307 CACTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.52
22 5 0.22
23 6 0.26
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAATTGAAAACAAAAATCTTTT
Found at i:64418771 original size:2 final size:2
Alignment explanation
Indices: 64418764--64418790 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
64418754 ATTTCATAAT
64418764 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
64418791 TTTAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64425433 original size:20 final size:20
Alignment explanation
Indices: 64425390--64425429 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
64425380 TGAAAACAAC
* *
64425390 ATATGTATATAGATATATAG
1 ATATGTATATAAATATATAA
64425410 ATATGTATATAAAT-TATAA
1 ATATGTATATAAATATATAA
64425429 A
1 A
64425430 ATATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
ATATGTATATAAATATATAA
Found at i:64427053 original size:25 final size:25
Alignment explanation
Indices: 64427020--64427181 Score: 89
Period size: 25 Copynumber: 6.6 Consensus size: 25
64427010 CTCTTTCGAT
* *
64427020 CCATTTAACGGGAAGCTCATGTGAG
1 CCATATAACGGGAAGCTCATATGAG
* * * *
64427045 CCATGTAACGGGAAGCTTATCTGGG
1 CCATATAACGGGAAGCTCATATGAG
** *
64427070 CTGTATAACGGGAAGCTCATAAGAG
1 CCATATAACGGGAAGCTCATATGAG
* ** **
64427095 CCATAT-TCAAGAAGCTCATGCGAG
1 CCATATAACGGGAAGCTCATATGAG
* * ** *
64427119 CCA-ATAACGCGTAGCTCCGAAGAG
1 CCATATAACGGGAAGCTCATATGAG
**
64427143 CCAT-TAACGGGAAGCTCCGGAT-AG
1 CCATATAACGGGAAGCT-CATATGAG
*
64427167 CCATATATCGGGAAG
1 CCATATAACGGGAAG
64427182 TTCAAGCAAG
Statistics
Matches: 102, Mismatches: 31, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
23 2 0.02
24 45 0.44
25 55 0.54
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (25 bp):
CCATATAACGGGAAGCTCATATGAG
Found at i:64427168 original size:24 final size:24
Alignment explanation
Indices: 64427116--64427181 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
64427106 AAGCTCATGC
* * *
64427116 GAGCCAATAACGCGTAGCTCCGAA
1 GAGCCATTAACGGGAAGCTCCGAA
*
64427140 GAGCCATTAACGGGAAGCTCCGGA
1 GAGCCATTAACGGGAAGCTCCGAA
* *
64427164 TAGCCATATATCGGGAAG
1 GAGCCAT-TAACGGGAAG
64427182 TTCAAGCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 26 0.74
25 9 0.26
ACGTcount: A:0.32, C:0.24, G:0.29, T:0.15
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCCGAA
Found at i:64428438 original size:15 final size:16
Alignment explanation
Indices: 64428410--64428440 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
64428400 TTGAAATAGC
64428410 ATTAAAACAATAACTA
1 ATTAAAACAATAACTA
64428426 ATTAAAA-AATAACTA
1 ATTAAAACAATAACTA
64428441 TTCACACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTAAAACAATAACTA
Found at i:64429521 original size:20 final size:21
Alignment explanation
Indices: 64429482--64429523 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
64429472 ACAAAATTAT
*
64429482 AAAATATAAAAATATTCATAA
1 AAAATATAAAAATATACATAA
64429503 AAAATATAAAAATA-ACATAA
1 AAAATATAAAAATATACATAA
64429523 A
1 A
64429524 GTACATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATATAAAAATATACATAA
Found at i:64435511 original size:4 final size:4
Alignment explanation
Indices: 64435502--64435553 Score: 54
Period size: 4 Copynumber: 13.0 Consensus size: 4
64435492 AGGAGAATAA
* *
64435502 AAAT AAAT AACAA AAAT AAAT AAAT AAAT -AA- AAAT AAAC AAAT AAATT
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T
64435550 AAAT
1 AAAT
64435554 CGAAAAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
3 4 0.10
4 29 0.73
5 7 0.17
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:64435518 original size:13 final size:12
Alignment explanation
Indices: 64435500--64435548 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
64435490 TAAGGAGAAT
64435500 AAAAATAAATAA
1 AAAAATAAATAA
64435512 CAAAAATAAATAA
1 -AAAAATAAATAA
*
64435525 ATAAATAAAAATAA
1 A-AAA-ATAAATAA
*
64435539 ACAAATAAAT
1 AAAAATAAAT
64435549 TAAATCGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 6 0.19
13 17 0.55
14 8 0.26
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAATAAATAA
Found at i:64435536 original size:18 final size:18
Alignment explanation
Indices: 64435502--64435548 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
64435492 AGGAGAATAA
*
64435502 AAATAAAT-AACAAAAAT
1 AAATAAATAAATAAAAAT
64435519 AAATAAATAAATAAAAAT
1 AAATAAATAAATAAAAAT
*
64435537 AAACAAATAAAT
1 AAATAAATAAAT
64435549 TAAATCGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATAAATAAATAAAAAT
Found at i:64436049 original size:19 final size:19
Alignment explanation
Indices: 64436006--64436045 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
64435996 GATTAAGGAG
64436006 AATAAAAATAACAAAAATA
1 AATAAAAATAACAAAAATA
*
64436025 AATAAAAATAA-ACAAATA
1 AATAAAAATAACAAAAATA
64436043 AAT
1 AAT
64436046 TAAATCGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (19 bp):
AATAAAAATAACAAAAATA
Found at i:64436446 original size:496 final size:496
Alignment explanation
Indices: 64435513--64436491 Score: 1780
Period size: 496 Copynumber: 2.0 Consensus size: 496
64435503 AATAAATAAC
*
64435513 AAAAATAAATAAATAAATAAAAATAAACAAATAAATTAAATCGAAAAACCAATAAGGAAGATTAA
1 AAAAATAAAAAAATAAATAAAAATAAACAAATAAATTAAATCGAAAAACCAATAAGGAAGATTAA
* *
64435578 CTCGCTTCAGGGTTTGTAACTAACTTCAGATTAGAGTTTTAGAGTGGATTAGTAATCGATTAACT
66 CTCGCTTAAGGGTTTGTAACTAACTTCAGATTAGAGTTTTACAGTGGATTAGTAATCGATTAACT
* *
64435643 AATTATTAGCTCCCGGCCTCAAATTAACGAGTAAATTGGTTGATACTCGCTTATCTCCCGACCTC
131 AATTATTACCTCCCGACCTCAAATTAACGAGTAAATTGGTTGATACTCGCTTATCTCCCGACCTC
*
64435708 ACTTTCTCAACCCAAATAAATTACAATTTACTTAGTTCGACTTATCTTTCGAACTCATCTAACCT
196 ACTTTCTCAACCCAAATAAATTACAATTTACTTAGTTCGACTTATCTTCCGAACTCATCTAACCT
*
64435773 ATGATAACTTATTAGGGTTGTGAAGCCTAACAATTTAAAAACACATAATTTATACCAACTAATCC
261 ATGATAACTTATTAGGGTTGTGAAGACTAACAATTTAAAAACACATAATTTATACCAACTAATCC
* * *
64435838 TTCTCGAGAAACCCTAAATCCTCCGTTAATCTCATCCCCATCCACTTGTTAATTTCCCTTAAGGG
326 TTCTCGAGAAACCCCAAATCCGCCATTAATCTCATCCCCATCCACTTGTTAATTTCCCTTAAGGG
64435903 ATTTAGCCACTCATGTTATTCATAATCTCAATTTCAATTGAATAAACTATGTGAGAAACACGATC
391 ATTTAGCCACTCATGTTATTCATAATCTCAATTTCAATTGAATAAACTATGTGAGAAACACGATC
64435968 GTTTCGGAGAAAAAAGGAGATTTGAATAGATTAAGGAGAAT
456 GTTTCGGAGAAAAAAGGAGATTTGAATAGATTAAGGAGAAT
64436009 AAAAATAACAAAAATAAATAAAAATAAACAAATAAATTAAATCGAAAAACCAATAAGGAAGATTA
1 AAAAATAA-AAAAATAAATAAAAATAAACAAATAAATTAAATCGAAAAACCAATAAGGAAGATTA
*
64436074 ACTTGCTTAAGGGTTTGTAACTAACTTCAGATTAGAGTTTTACAGTGGATTAGTAATCGATTAAC
65 ACTCGCTTAAGGGTTTGTAACTAACTTCAGATTAGAGTTTTACAGTGGATTAGTAATCGATTAAC
64436139 TAATTATTACCTCCCGACCTCAAATTAACGAGTAAATTGGTTGATACTCGCTTATCT-CCGACCT
130 TAATTATTACCTCCCGACCTCAAATTAACGAGTAAATTGGTTGATACTCGCTTATCTCCCGACCT
* *
64436203 CACTTTCTCAACGCAAATAAATTACAATTTACTTAGTTCGACTTATCTTCCGACCTCATCTAACC
195 CACTTTCTCAACCCAAATAAATTACAATTTACTTAGTTCGACTTATCTTCCGAACTCATCTAACC
*
64436268 TATGATAACTTATTAGGGTTGTGAAGACTAACAATTTAAGAACACATAATTTATACCAACTAATC
260 TATGATAACTTATTAGGGTTGTGAAGACTAACAATTTAAAAACACATAATTTATACCAACTAATC
*
64436333 CTTCTCGAGAAACCCCAAATCCGCCATTAATCTCATCCTCATCCACTTGTTAATTTCCCTTAAGG
325 CTTCTCGAGAAACCCCAAATCCGCCATTAATCTCATCCCCATCCACTTGTTAATTTCCCTTAAGG
64436398 GATTTAGCCACTCATGTTATTCATAATCTCAATTTCAATTGAATAAACTATGTGAGAAACACGAT
390 GATTTAGCCACTCATGTTATTCATAATCTCAATTTCAATTGAATAAACTATGTGAGAAACACGAT
* * *
64436463 CGTTTTGGAGAGAAAATGAGATTTGAATA
455 CGTTTCGGAGAAAAAAGGAGATTTGAATA
64436492 ATTGTGGATT
Statistics
Matches: 464, Mismatches: 18, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
496 292 0.63
497 172 0.37
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.31
Consensus pattern (496 bp):
AAAAATAAAAAAATAAATAAAAATAAACAAATAAATTAAATCGAAAAACCAATAAGGAAGATTAA
CTCGCTTAAGGGTTTGTAACTAACTTCAGATTAGAGTTTTACAGTGGATTAGTAATCGATTAACT
AATTATTACCTCCCGACCTCAAATTAACGAGTAAATTGGTTGATACTCGCTTATCTCCCGACCTC
ACTTTCTCAACCCAAATAAATTACAATTTACTTAGTTCGACTTATCTTCCGAACTCATCTAACCT
ATGATAACTTATTAGGGTTGTGAAGACTAACAATTTAAAAACACATAATTTATACCAACTAATCC
TTCTCGAGAAACCCCAAATCCGCCATTAATCTCATCCCCATCCACTTGTTAATTTCCCTTAAGGG
ATTTAGCCACTCATGTTATTCATAATCTCAATTTCAATTGAATAAACTATGTGAGAAACACGATC
GTTTCGGAGAAAAAAGGAGATTTGAATAGATTAAGGAGAAT
Found at i:64438161 original size:2 final size:2
Alignment explanation
Indices: 64438154--64438180 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
64438144 AAACACGCAA
64438154 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
64438181 GAAACTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64441802 original size:48 final size:48
Alignment explanation
Indices: 64441682--64441803 Score: 129
Period size: 48 Copynumber: 2.5 Consensus size: 48
64441672 TTGTCTGTGG
* * * *
64441682 TTAAATGATTGATTTGCCCGTGATGTAAATAAATGATTTGTCCTAGAT
1 TTAAATGACTGATTTGTCTGTGATTTAAATAAATGATTTGTCCTAGAT
* * * * * **
64441730 GTAAATGACTGTTTTATCTGTGATTTAAATGATTGATTTGTTTGTA-AT
1 TTAAATGACTGATTTGTCTGTGATTTAAATAAATGATTTG-TCCTAGAT
64441778 TTAAATGACTGATTTGTCTGTGATTT
1 TTAAATGACTGATTTGTCTGTGATTT
64441804 GTATGACTTA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
48 56 0.95
49 3 0.05
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (48 bp):
TTAAATGACTGATTTGTCTGTGATTTAAATAAATGATTTGTCCTAGAT
Found at i:64441811 original size:24 final size:24
Alignment explanation
Indices: 64441671--64441803 Score: 117
Period size: 24 Copynumber: 5.6 Consensus size: 24
64441661 TCTGAATACT
* *
64441671 TTTGTCTGTG-GTTAAATGATTGA
1 TTTGTCTGTGATTTAAATGACTGA
* * * * *
64441694 TTTGCCCGTGATGTAAATAAATGA
1 TTTGTCTGTGATTTAAATGACTGA
* * *
64441718 TTTGTCCT-AGATGTAAATGACTGT
1 TTTGT-CTGTGATTTAAATGACTGA
* *
64441742 TTTATCTGTGATTTAAATGATTGA
1 TTTGTCTGTGATTTAAATGACTGA
* *
64441766 TTTGTTTGTAATTTAAATGACTGA
1 TTTGTCTGTGATTTAAATGACTGA
64441790 TTTGTCTGTGATTT
1 TTTGTCTGTGATTT
64441804 GTATGACTTA
Statistics
Matches: 84, Mismatches: 23, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
23 10 0.12
24 73 0.87
25 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.47
Consensus pattern (24 bp):
TTTGTCTGTGATTTAAATGACTGA
Found at i:64441917 original size:27 final size:27
Alignment explanation
Indices: 64441879--64441941 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
64441869 ATAGAGAAAG
64441879 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTGGCT-TGGCCACATA
64441904 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
64441932 TACTGTTACT
1 TACTGTTACT
64441942 AGCAGCTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 1 0.03
26 5 0.15
27 26 0.76
28 2 0.06
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.33
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:64441949 original size:27 final size:27
Alignment explanation
Indices: 64441897--64441949 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
64441887 TGGTGGCTCT
* **
64441897 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAATCACTGTTACTAGCAGCTTG
64441924 GCCACATAT-ACTGTTACTAGCAGCTT
1 GCCACA-ATCACTGTTACTAGCAGCTT
64441950 TGCTGCGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTGTTACTAGCAGCTTG
Found at i:64446028 original size:27 final size:27
Alignment explanation
Indices: 64445995--64446061 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
64445985 GCAATATACG
* *
64445995 AAAGGAATGCCTTCATGGCAAACTTTA
1 AAAGGAATGCCTTCATGACAAACTCTA
*
64446022 AAGGGAATGCCTTCATGACAAACTCTA
1 AAAGGAATGCCTTCATGACAAACTCTA
64446049 AAAGGAATGCCTT
1 AAAGGAATGCCTT
64446062 GACGGCGTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (27 bp):
AAAGGAATGCCTTCATGACAAACTCTA
Found at i:64468241 original size:39 final size:39
Alignment explanation
Indices: 64468186--64468365 Score: 209
Period size: 39 Copynumber: 4.6 Consensus size: 39
64468176 AACATGTTTT
* * *
64468186 TGAGTATTGTGGTATATGTTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
64468225 TGAGTATTGTGATATATGCCTGAATGTTATGTGATTGTA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* ** *
64468264 TGAGTATTGTTATATATGCTTAAACATTATGTAATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
64468303 TGAGTATTGTGATATATGCATAAAGGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
64468342 T-ATGTAATGTGATACATGTTTAAA
1 TGA-GTATTGTGATATATGCTTAAA
64468366 AGTGATTATC
Statistics
Matches: 120, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
38 1 0.01
39 119 0.99
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.44
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:64469136 original size:42 final size:42
Alignment explanation
Indices: 64469086--64469180 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
64469076 TTTCCCAGTG
64469086 GTATCGATACCACTTGAGAGAATTACTAACACCATTT-TTATA
1 GTATCGATACCACTTGAGAGAATTACTAACACC-TTTGTTATA
* * *
64469128 GTATCGATACCACTTGAGAGAATTATTGATACCTTTGTTATA
1 GTATCGATACCACTTGAGAGAATTACTAACACCTTTGTTATA
64469170 GTATCGATACC
1 GTATCGATACC
64469181 TACATAATTG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
41 3 0.06
42 46 0.94
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (42 bp):
GTATCGATACCACTTGAGAGAATTACTAACACCTTTGTTATA
Found at i:64470045 original size:22 final size:22
Alignment explanation
Indices: 64470017--64470122 Score: 140
Period size: 22 Copynumber: 4.8 Consensus size: 22
64470007 TTTATTGTTC
*
64470017 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
64470039 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
64470061 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
64470083 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
64470105 AAACATGAGAGCTTAGTA
1 AAACATGAGAGCTTAGTA
64470123 TATTTTTGGT
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 73 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:64470231 original size:18 final size:18
Alignment explanation
Indices: 64470208--64470242 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
64470198 TTGAAAATTT
64470208 GGATTTGAGTAGAAAAGG
1 GGATTTGAGTAGAAAAGG
64470226 GGATTTGAGTAGAAAAG
1 GGATTTGAGTAGAAAAG
64470243 CATCCAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.37, T:0.23
Consensus pattern (18 bp):
GGATTTGAGTAGAAAAGG
Found at i:64471421 original size:73 final size:73
Alignment explanation
Indices: 64471320--64471466 Score: 267
Period size: 73 Copynumber: 2.0 Consensus size: 73
64471310 TTATATCATG
64471320 AGCAAAGTTTCCTTTCCTAAATACACCACCACACAAGGTTAGTAGGTGTATAGATAAGCATATAA
1 AGCAAAGTTTCCTTTCCTAAATACACCACCACACAAGGTTAGTAGGTGTATAGATAAGCATATAA
64471385 ATCCAACC
66 ATCCAACC
* * *
64471393 AGCAAAGTTTCCTTTCCTAAATACACCACCATACAAGGTTAGTAGGTGTATAGGTAAGCATCTAA
1 AGCAAAGTTTCCTTTCCTAAATACACCACCACACAAGGTTAGTAGGTGTATAGATAAGCATATAA
64471458 ATCCAACC
66 ATCCAACC
64471466 A
1 A
64471467 ATTTGTGAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (73 bp):
AGCAAAGTTTCCTTTCCTAAATACACCACCACACAAGGTTAGTAGGTGTATAGATAAGCATATAA
ATCCAACC
Found at i:64472307 original size:39 final size:39
Alignment explanation
Indices: 64472235--64472310 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
64472225 TTTCTTTATC
*
64472235 TAAATAGTAATTTTATTCAATTAATACTATTCCAACACT
1 TAAATAGTAATTTTATTCAATTAATACCATTCCAACACT
*
64472274 TAAATAAGTAATTTTATAT-AATTAAT-CCCTTCCAACA
1 TAAAT-AGTAATTTTAT-TCAATTAATACCATTCCAACA
64472311 TTATTTTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 14 0.42
40 18 0.55
41 1 0.03
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (39 bp):
TAAATAGTAATTTTATTCAATTAATACCATTCCAACACT
Found at i:64481211 original size:11 final size:11
Alignment explanation
Indices: 64481195--64481221 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
64481185 AATCCCGTAG
64481195 ATAATAAAATA
1 ATAATAAAATA
64481206 ATAATAAAATA
1 ATAATAAAATA
64481217 ATAAT
1 ATAAT
64481222 TTACTAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAATAAAATA
Found at i:64481391 original size:18 final size:19
Alignment explanation
Indices: 64481357--64481394 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
64481347 AAATCTTGTT
64481357 ATTAAACTTGGTGATGTGA
1 ATTAAACTTGGTGATGTGA
64481376 ATTAAA-TTGGAT-ATGTGA
1 ATTAAACTTGG-TGATGTGA
64481394 A
1 A
64481395 CACTTAACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (19 bp):
ATTAAACTTGGTGATGTGA
Found at i:64489622 original size:18 final size:18
Alignment explanation
Indices: 64489595--64489631 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
64489585 ATTGAGTAAG
*
64489595 AAAAGTGATTAATTTTAT
1 AAAAGCGATTAATTTTAT
64489613 AAAAGCGATTAATTTTAT
1 AAAAGCGATTAATTTTAT
64489631 A
1 A
64489632 TGCTCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.41
Consensus pattern (18 bp):
AAAAGCGATTAATTTTAT
Found at i:64491701 original size:3 final size:3
Alignment explanation
Indices: 64491693--64491749 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
64491683 GCATTAATGG
64491693 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
64491741 TAA AAA TAA
1 TAA TAA TAA
64491750 AATGACTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:64491750 original size:6 final size:6
Alignment explanation
Indices: 64491697--64491801 Score: 57
Period size: 6 Copynumber: 16.0 Consensus size: 6
64491687 TAATGGTAAT
* * * * * * *
64491697 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
*
64491745 AATAAA ATGACTAAA AATAAA TAGCATAAA AATAAA GAAAATAA AATAATA
1 AATAAA A--A-TAAA AATAAA -A--ATAAA AATAAA -AATA-AA AATAA-A
64491796 AATAAA
1 AATAAA
64491802 TAAATAAGAA
Statistics
Matches: 87, Mismatches: 3, Indels: 18
0.81 0.03 0.17
Matches are distributed among these distances:
6 59 0.68
7 14 0.16
8 4 0.05
9 10 0.11
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (6 bp):
AATAAA
Found at i:64491808 original size:15 final size:13
Alignment explanation
Indices: 64491693--64491800 Score: 85
Period size: 12 Copynumber: 8.8 Consensus size: 13
64491683 GCATTAATGG
64491693 TAAT-AATAATAA
1 TAATAAATAATAA
64491705 TAAT-AATAATAA
1 TAATAAATAATAA
64491717 TAAT-AATAATAA
1 TAATAAATAATAA
64491729 TAAT-AATAATAA
1 TAATAAATAATAA
64491741 TAA-AAATAA-AA
1 TAATAAATAATAA
*
64491752 TGACTAAA-AATAAA
1 T-AATAAATAAT-AA
64491766 TAGCATAAA-AATAA
1 TA--ATAAATAATAA
64491780 -AGA-AAATAA-AA
1 TA-ATAAATAATAA
64491791 TAATAAATAA
1 TAATAAATAA
64491801 ATAAATAAGA
Statistics
Matches: 83, Mismatches: 3, Indels: 20
0.78 0.03 0.19
Matches are distributed among these distances:
11 9 0.11
12 57 0.69
13 5 0.06
14 5 0.06
15 7 0.08
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (13 bp):
TAATAAATAATAA
Found at i:64503018 original size:26 final size:26
Alignment explanation
Indices: 64502972--64503021 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
64502962 TGCATTTCCC
*
64502972 CTAATGCAAAAGAAAACTAAAAACTA
1 CTAATGCAAAAGAAAAATAAAAACTA
*
64502998 CTAATG-AAAATAAAGAATAAAAAC
1 CTAATGCAAAAGAAA-AATAAAAAC
64503022 ATAAAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.64, C:0.12, G:0.08, T:0.16
Consensus pattern (26 bp):
CTAATGCAAAAGAAAAATAAAAACTA
Done.