Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 102 of 218
Found at i:29570810 original size:21 final size:21
Alignment explanation
Indices: 29570786--29570828 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29570776 TGGAATTTTT
*
29570786 AAGTTAAACAAATTTTTGAAA
1 AAGTTAAACAAAGTTTTGAAA
* *
29570807 AAGTTAAATAGAGTTTTGAAA
1 AAGTTAAACAAAGTTTTGAAA
29570828 A
1 A
29570829 CTGTAACTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (21 bp):
AAGTTAAACAAAGTTTTGAAA
Found at i:29574207 original size:40 final size:42
Alignment explanation
Indices: 29574122--29574212 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 42
29574112 TACAAAGTAG
* *
29574122 TATCTAAATATTAATTGAGTAAAAGTAAAGTTAAACAATTACAA
1 TATCTAAATATTAATTAAGT--AAGTAAACTTAAACAATTACAA
* *
29574166 TATCTAAATATTAATTAAGT-A-TAAACTTAAATATTTACAA
1 TATCTAAATATTAATTAAGTAAGTAAACTTAAACAATTACAA
29574206 TATCTAA
1 TATCTAA
29574213 TACAAATTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 23 0.53
41 1 0.02
44 19 0.44
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (42 bp):
TATCTAAATATTAATTAAGTAAGTAAACTTAAACAATTACAA
Found at i:29577945 original size:43 final size:43
Alignment explanation
Indices: 29577846--29577963 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 43
29577836 GCAGCTTGTC
* * * *
29577846 TGCACCGTTTAGTGGTTAATCCACACCATATTAGTAGCTTATT
1 TGCAACGTTTAGTGGTTAATCCACATCGTACTAGTAGCTTATT
** *
29577889 TGC-ACTGAATAGTGGTTTATCCACATCGTACTAGTAG-TTCATT
1 TGCAAC-GTTTAGTGGTTAATCCACATCGTACTAGTAGCTT-ATT
* *
29577932 TGCAACGTTTAGTGGTTCATCCACATTGTACT
1 TGCAACGTTTAGTGGTTAATCCACATCGTACT
29577964 GTAAAGGTAG
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
42 3 0.05
43 56 0.92
44 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (43 bp):
TGCAACGTTTAGTGGTTAATCCACATCGTACTAGTAGCTTATT
Found at i:29594441 original size:62 final size:62
Alignment explanation
Indices: 29594336--29594522 Score: 205
Period size: 62 Copynumber: 3.0 Consensus size: 62
29594326 CATGACTCAT
* * * * * *
29594336 ACGGCTTGGGTACACGCCCATGTCCCTAATCGTGTTGTTTTATATCACAAACAGTGAGTTAC
1 ACGGCTTGGGTACAAGCCCGTGTCCCTAGTCGTGTGGTCTTATACCACAAACAGTGAGTTAC
* * * * *
29594398 ACGGCTTGGGTACATGCCCGTGTCCCTGGCCGTGTGGTCTTATACCACAAACAGTAAGGTAC
1 ACGGCTTGGGTACAAGCCCGTGTCCCTAGTCGTGTGGTCTTATACCACAAACAGTGAGTTAC
* * * * * *
29594460 ACGGCCTGAGCACAAGCCTGTGTCCCAAGTCGTGTGGTCTTGA-CCCACAAACAGTGAGTTAC
1 ACGGCTTGGGTACAAGCCCGTGTCCCTAGTCGTGTGGTCTT-ATACCACAAACAGTGAGTTAC
29594522 A
1 A
29594523 GGGCCTGGAC
Statistics
Matches: 103, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
62 102 0.99
63 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.25
Consensus pattern (62 bp):
ACGGCTTGGGTACAAGCCCGTGTCCCTAGTCGTGTGGTCTTATACCACAAACAGTGAGTTAC
Found at i:29594528 original size:62 final size:62
Alignment explanation
Indices: 29594366--29594542 Score: 178
Period size: 62 Copynumber: 2.9 Consensus size: 62
29594356 TGTCCCTAAT
* * * * * * * **
29594366 CGTGTTGTTTTATATCACAAACAGTGAGTTACACGGCTTGGGTACATGCCCGTGTCCCTGGC
1 CGTGTGGTCTTATACCACAAACAGTGAGTTACACGGCCTGAGCACAAGCCCGTGTCCCAAGC
* * * *
29594428 CGTGTGGTCTTATACCACAAACAGTAAGGTACACGGCCTGAGCACAAGCCTGTGTCCCAAGT
1 CGTGTGGTCTTATACCACAAACAGTGAGTTACACGGCCTGAGCACAAGCCCGTGTCCCAAGC
* * *
29594490 CGTGTGGTCTTGA-CCCACAAACAGTGAGTTACAGGGCCTG-GACACACGCCCGT
1 CGTGTGGTCTT-ATACCACAAACAGTGAGTTACACGGCCTGAG-CACAAGCCCGT
29594543 ATCCATGGCT
Statistics
Matches: 94, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
61 1 0.01
62 92 0.98
63 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (62 bp):
CGTGTGGTCTTATACCACAAACAGTGAGTTACACGGCCTGAGCACAAGCCCGTGTCCCAAGC
Found at i:29596056 original size:16 final size:16
Alignment explanation
Indices: 29596037--29596072 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29596027 ATTTGTTTTT
*
29596037 GTTCTGTATTCAGGTA
1 GTTCTGTATTCAGCTA
*
29596053 GTTCTGTATTTAGCTA
1 GTTCTGTATTCAGCTA
29596069 GTTC
1 GTTC
29596073 ATATTCTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (16 bp):
GTTCTGTATTCAGCTA
Found at i:29596330 original size:16 final size:17
Alignment explanation
Indices: 29596309--29596342 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
29596299 AAACACAACA
29596309 TTTTTAT-ATTTAAAAT
1 TTTTTATAATTTAAAAT
29596325 TTTTTATAATTTAAAAT
1 TTTTTATAATTTAAAAT
29596342 T
1 T
29596343 AAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTATAATTTAAAAT
Found at i:29596840 original size:20 final size:20
Alignment explanation
Indices: 29596799--29596836 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
29596789 TTGAAGTTAC
*
29596799 AAATTATATAAAATAACTAT
1 AAATTATATAAAATAAATAT
*
29596819 AAATTATA-ACAATAAATA
1 AAATTATATAAAATAAATA
29596837 ATAATTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTATATAAAATAAATAT
Found at i:29600305 original size:50 final size:50
Alignment explanation
Indices: 29600201--29600296 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 50
29600191 ACATTAAGGG
* * * *
29600201 AATGAGA--TCCCATGTAAAACCATGTCTGGGACATGGCGTTGGCTCCAA
1 AATGAGATGTCCCATGTAAAACCATGTCAGGGACATGGCATGGGCACCAA
* *
29600249 AATGAGATGTCCCTTGTAAGACCATGTCAGGGACATGGCATGGGCACC
1 AATGAGATGTCCCATGTAAAACCATGTCAGGGACATGGCATGGGCACC
29600297 GATGTGAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
48 7 0.17
50 33 0.82
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (50 bp):
AATGAGATGTCCCATGTAAAACCATGTCAGGGACATGGCATGGGCACCAA
Found at i:29606488 original size:23 final size:23
Alignment explanation
Indices: 29606433--29606509 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
29606423 AGTGTTATTG
29606433 ATCAGTGGTAGCTTCGGCTACATT
1 ATCAGTGGTAGCTTCGGCTACA-T
* *
29606457 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
29606480 ATCAGTGGTAGCTTCGTCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
29606503 ATCAGTG
1 ATCAGTG
29606510 TGGCACTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 28 0.58
24 20 0.42
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:29610513 original size:42 final size:42
Alignment explanation
Indices: 29610375--29610561 Score: 186
Period size: 43 Copynumber: 4.4 Consensus size: 42
29610365 CGATGGATTT
* * * *
29610375 AGCACTTAGCAACCACCTTAAATTCAGTGATACGG-GGAATC
1 AGCACATAGCAACCACCTTCAATTCAATAATACGGTGGAATC
* *
29610416 AGCACATAGCAACC-CCTTTCACAGTCTAA-GATACGGTGGAATC
1 AGCACATAGCAACCACC-TTCA-ATTC-AATAATACGGTGGAATC
* * *
29610459 ACCACTTTGCAACCACCTTCATATTCAATAATACGG-GGAATC
1 AGCACATAGCAACCACCTTCA-ATTCAATAATACGGTGGAATC
* *
29610501 AGCACATAGCAACC-CCTTTCCAATTTAAAAATACGGTGGAATC
1 AGCACATAGCAACCACC-TT-CAATTCAATAATACGGTGGAATC
29610544 AGCACATAGCAACCACCT
1 AGCACATAGCAACCACCT
29610562 CTAGAGTCAG
Statistics
Matches: 121, Mismatches: 15, Indels: 18
0.79 0.10 0.12
Matches are distributed among these distances:
40 2 0.02
41 18 0.15
42 43 0.36
43 54 0.45
44 4 0.03
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.22
Consensus pattern (42 bp):
AGCACATAGCAACCACCTTCAATTCAATAATACGGTGGAATC
Found at i:29610519 original size:85 final size:85
Alignment explanation
Indices: 29610377--29610602 Score: 280
Period size: 85 Copynumber: 2.7 Consensus size: 85
29610367 ATGGATTTAG
* *
29610377 CACTTAGCAACCACCTT-AAATTCAGTGATACGGGGAATCAGCACATAGCAACCCCTTTCACAGT
1 CACTTAGCAACCACCTTCAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCTTTC-CAAT
*
29610441 CT-AAGATACGGTGGAATCAC
65 CTAAAAATACGGTGGAATCAC
* * * *
29610461 CACTTTGCAACCACCTTCATATTCAATAATACGGGGAATCAGCACATAGCAACCCCTTTCCAATT
1 CACTTAGCAACCACCTTCAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCTTTCCAATC
*
29610526 TAAAAATACGGTGGAATCAG
66 TAAAAATACGGTGGAATCAC
* * * * *
29610546 CACATAGCAACCACC-TCTAGAGTCAGTAA-ATCGGGGAATCAACACTTAGCAACCCCT
1 CACTTAGCAACCACCTTC-AAATTCAGTAATA-CGGGGAATCAGCACATAGCAACCCCT
29610603 CGGGGAATCA
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
84 23 0.19
85 100 0.81
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.22
Consensus pattern (85 bp):
CACTTAGCAACCACCTTCAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCTTTCCAATC
TAAAAATACGGTGGAATCAC
Found at i:29610612 original size:26 final size:26
Alignment explanation
Indices: 29610576--29610628 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
29610566 AGTCAGTAAA
29610576 TCGGGGAATCAACACTTAGCAACCCC
1 TCGGGGAATCAACACTTAGCAACCCC
*
29610602 TCGGGGAATCAACACTTAGCGACCCC
1 TCGGGGAATCAACACTTAGCAACCCC
29610628 T
1 T
29610629 TTTTATTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.34, G:0.21, T:0.17
Consensus pattern (26 bp):
TCGGGGAATCAACACTTAGCAACCCC
Found at i:29618076 original size:42 final size:41
Alignment explanation
Indices: 29617940--29618151 Score: 205
Period size: 43 Copynumber: 5.0 Consensus size: 41
29617930 CGATGGATTT
* * * *
29617940 AGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATC
1 AGCACATAGCAACCACCTTTAATTCAATAATACGGGGAATC
* *
29617981 AGCACATAGCAACC-CCTTTCACAATCAA-AGATACGGTAGAATC
1 AGCACATAGCAACCACCTTT-A-ATTCAATA-ATACGG-GGAATC
**
29618024 AGCAGTTAGCAACCACCTTTATATTCAATAATACGGGGAATC
1 AGCACATAGCAACCACCTTTA-ATTCAATAATACGGGGAATC
*
29618066 AGCACATAGCAACC-CCTTTCCAATTCAAAAATACGGTGGAATC
1 AGCACATAGCAACCACCTTT--AATTCAATAATACGG-GGAATC
* * * *
29618109 AGCACATAGCAACCACCTCTAGAGTCAGTAATTCGGGGAATC
1 AGCACATAGCAACCACCTTTA-ATTCAATAATACGGGGAATC
29618151 A
1 A
29618152 ACACTTACCA
Statistics
Matches: 141, Mismatches: 19, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
40 4 0.03
41 19 0.13
42 48 0.34
43 60 0.43
44 10 0.07
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (41 bp):
AGCACATAGCAACCACCTTTAATTCAATAATACGGGGAATC
Found at i:29618094 original size:85 final size:85
Alignment explanation
Indices: 29617940--29618167 Score: 307
Period size: 85 Copynumber: 2.7 Consensus size: 85
29617930 CGATGGATTT
*
29617940 AGCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCCCTTTCACA
1 AGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCTTTCACA
*
29618004 ATCAAAGATACGGTAGAATC
66 ATCAAAAATACGGTAGAATC
* * *
29618024 AGCAGTTAGCAACCACCTTTATATTCAATAATACGGGGAATCAGCACATAGCAACCCCTTTC-CA
1 AGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCTTTCACA
*
29618088 ATTCAAAAATACGGTGGAATC
66 A-TCAAAAATACGGTAGAATC
* * * * * * * *
29618109 AGCACATAGCAACCACCTCTAGAGTCAGTAATTCGGGGAATCAACACTTACCAACCCCT
1 AGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCT
29618168 CGGGGAATCT
Statistics
Matches: 126, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
84 19 0.15
85 107 0.85
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (85 bp):
AGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCTTTCACA
ATCAAAAATACGGTAGAATC
Found at i:29622421 original size:50 final size:50
Alignment explanation
Indices: 29622332--29622446 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
29622322 GATCACATGA
* * * *
29622332 AAGACCATGTCTGGGACATGGCGTTGGCGCCGAGATGAGAAGTCCCCCGT
1 AAGACCATGTCTGGGACATGGCGATGGCACCGAGATGAGAACTCCCACGT
* *
29622382 AAGACCATGTCTGGGACATGGC-ATGGACACTGATG-TGAGAACTCCCATGT
1 AAGACCATGTCTGGGACATGGCGATGG-CACCGA-GATGAGAACTCCCACGT
*
29622432 AAGACCATATCTGGG
1 AAGACCATGTCTGGG
29622447 CTATGACATT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
49 3 0.05
50 52 0.93
51 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AAGACCATGTCTGGGACATGGCGATGGCACCGAGATGAGAACTCCCACGT
Found at i:29636934 original size:16 final size:16
Alignment explanation
Indices: 29636901--29636934 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29636891 GTAAATTCTC
*
29636901 AAAAAGATATGAAAAG
1 AAAAAGATAGGAAAAG
*
29636917 AAAAAGATAGGAACAG
1 AAAAAGATAGGAAAAG
29636933 AA
1 AA
29636935 GAGAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.21, T:0.09
Consensus pattern (16 bp):
AAAAAGATAGGAAAAG
Found at i:29640351 original size:201 final size:202
Alignment explanation
Indices: 29640006--29640464 Score: 749
Period size: 201 Copynumber: 2.3 Consensus size: 202
29639996 TATTTTGCCA
* *
29640006 TCTGTTTTTCAATAATAGTTTTCCAAGACTTAAATGCGAAAAACACATCGCTTTTCTGCTTCAGG
1 TCTGTTTTTCAATAATAGTTTTCCAAGACTTAAATGCGAAAAACACATCACTTTTCTACTTCAGG
29640071 AAGAACGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGCTCCACCTCT
66 AAGAACGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGCTCCACCTCT
*
29640136 CGAAAGCACTCTAGATGGCCTCCACAAATCAGAATGAATATACTCCAGCGTTCCCTTCATGTTAT
131 CGAAAGCACTCTAGATGGCCTCCACAAATCAGAATGAATATACTCCAACGTTCCCTTCATGTTAT
29640201 GGC-TTT
196 GGCTTTT
* *
29640207 TCTGTTTTTCAATAATAGTTTTCCAAGACTGAAATGCGAAAAACACATCACTTTTCTACTTTAGG
1 TCTGTTTTTCAATAATAGTTTTCCAAGACTTAAATGCGAAAAACACATCACTTTTCTACTTCAGG
* *
29640272 AAGAACGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGGTTCACCTCT
66 AAGAACGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGCTCCACCTCT
* * * * *
29640337 CGAAGGCACTCTAGATGGCCTCCACAGATCAGAATTAATATACTCCAATGTTCCCTTCCTGTTAT
131 CGAAAGCACTCTAGATGGCCTCCACAAATCAGAATGAATATACTCCAACGTTCCCTTCATGTTAT
29640402 GGCTTTT
196 GGCTTTT
* * * * * *
29640409 TTTGTTTTTCAATAAGAGTATTCCAAGACTTAAATGTGGAAGACACATCACTTTTC
1 TCTGTTTTTCAATAATAGTTTTCCAAGACTTAAATGCGAAAAACACATCACTTTTC
29640465 AGAATTAAAT
Statistics
Matches: 238, Mismatches: 19, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
201 186 0.78
202 52 0.22
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Consensus pattern (202 bp):
TCTGTTTTTCAATAATAGTTTTCCAAGACTTAAATGCGAAAAACACATCACTTTTCTACTTCAGG
AAGAACGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGCTCCACCTCT
CGAAAGCACTCTAGATGGCCTCCACAAATCAGAATGAATATACTCCAACGTTCCCTTCATGTTAT
GGCTTTT
Found at i:29643191 original size:26 final size:26
Alignment explanation
Indices: 29643162--29643242 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
29643152 AACACACCAA
*
29643162 TATCGCAGCAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
* *
29643188 TATCGCAGCAAAGCTACCACTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
* *
29643214 TATTGCAACAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
29643240 TAT
1 TAT
29643243 ACTTTCTCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:29643426 original size:27 final size:27
Alignment explanation
Indices: 29643406--29644032 Score: 558
Period size: 27 Copynumber: 23.4 Consensus size: 27
29643396 GGGTATAACA
*
29643406 GTCATTTTACCCTATGAGGGTATTTCA
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
29643433 GTCATTTTATCCTATGA-GGTATCTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
29643459 GTCATTTTACCCTAT-AGGGGTATCTCG
1 GTCATTTTACCCTATGA-GGGTATTTCG
* *
29643486 ATCATTTTACCCAATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
29643513 GTCA-TTTACCCTATGGGGGTATCTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
29643539 ATCATTTTACCCTATAAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
29643566 GTCATTTTACCCTATGGGGGTATTCCA
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
29643593 GTTATTTTACCTTAT-AGGGGTATTTCA
1 GTCATTTTACCCTATGA-GGGTATTTCG
** * *
29643620 GTCATGCTACTCTAT-AGGGGTATTCCG
1 GTCATTTTACCCTATGA-GGGTATTTCG
* * * *
29643647 ATCATTTTATCCTATCAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * * *
29643674 ATTATTTTACTCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *** * *
29643701 GTTATTCTATATTATGGGGGTATTTCA
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
29643728 GTCATTTTACCCTGT-AGGGGTATTTCT
1 GTCATTTTACCCTATGA-GGGTATTTCG
*
29643755 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
29643782 GTCATTCTACCCTATG-GGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
29643808 GTCATTCTACCCTATG-GGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
29643834 GTCATTTTACCGTATG-GAGGTATTTCT
1 GTCATTTTACCCTATGAG-GGTATTTCG
* *
29643861 ATCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * * * *
29643888 ATCTTTTTATCCTATG-GGCATTTTTCG
1 GTCATTTTACCCTATGAGG-GTATTTCG
*
29643915 GTCATTCTACCCTAT-AGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
** * *
29643941 GTGTTTTTACCCTATGGGGGTTTTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
29643968 GTCATTCTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
29643995 GTCATTTTATCCTGT-AGGGATATTTCG
1 GTCATTTTACCCTATGAGGG-TATTTCG
*
29644022 ATCATTTTACC
1 GTCATTTTACC
29644033 TATTTTGTGG
Statistics
Matches: 489, Mismatches: 97, Indels: 28
0.80 0.16 0.05
Matches are distributed among these distances:
25 1 0.00
26 117 0.24
27 368 0.75
28 3 0.01
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:29644050 original size:107 final size:106
Alignment explanation
Indices: 29643409--29644032 Score: 520
Period size: 107 Copynumber: 5.8 Consensus size: 106
29643399 TATAACAGTC
* * * * * *
29643409 ATTTTACCCTATGAGGGTATTTCAGTCATTTTATCCTAT-GAGGTATCTCGGTCATTTTACCCTA
1 ATTTTACCCTATGGGGGTATTTCTGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCCTA
* * * * * *
29643473 TAGGGGTATCTCGATCATTTTACCCAATGAGGGTATTTCGGTC
66 T-GGGATATTTCGGTCATTCTACCCTAT-AGGGTATTTCGGTG
* ** * *
29643516 A-TTTACCCTATGGGGGTATCTC-GATCATTTTACCCTATAAGGGTATTTTGGTCATTTTACCCT
1 ATTTTACCCTATGGGGGTATTTCTG-TCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCCT
* * * * * * * *
29643579 ATGGGGGTATTCCAGTTATTTTACCTTATAGGGGTATTTCAGTC
65 AT-GGGATATTTCGGTCATTCTACCCTATA-GGGTATTTCGGTG
** * * * * ** * * *
29643623 ATGCTACTCTATAGGGGTA-TTCCGATCATTTTATCCTATCAGGGTATTTTGATTATTTTA-CTC
1 ATTTTACCCTATGGGGGTATTTCTG-TCATTTTACCCTATGGGGGTATTTCGGTCATTTTATC-C
* * * *** * * *
29643686 TATGAGGGTATTTTGGTTATTCTATATTATGGGGGTATTTCAGTC
64 TATG-GGATATTTCGGTCATTCTACCCTAT-AGGGTATTTCGGTG
* * * *
29643731 ATTTTACCCTGTAGGGGTATTTCTGTCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTA
1 ATTTTACCCTATGGGGGTATTTCTGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCCTA
* * *
29643796 TGGGGTATTTCGGTCATTCTACCCTATGGGGTATTTCGGTC
66 TGGGATATTTCGGTCATTCTACCCTATAGGGTATTTCGGTG
* * * * *
29643837 ATTTTACCGTATGGAGGTATTTCTATCATTTTACCCTATGGGGGTATTTCGATCTTTTTATCCTA
1 ATTTTACCCTATGGGGGTATTTCTGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCCTA
*
29643902 TGGGCATTTTTCGGTCATTCTACCCTATAGGGTATTTCGGTG
66 TGGG-ATATTTCGGTCATTCTACCCTATAGGGTATTTCGGTG
* * * * * *
29643944 TTTTTACCCTATGGGGGTTTTTCGGTCATTCTACCCTATGGGGGTATTTTGGTCATTTTATCCTG
1 ATTTTACCCTATGGGGGTATTTCTGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCCTA
* *
29644009 TAGGGATATTTCGATCATTTTACC
66 T-GGGATATTTCGGTCATTCTACC
29644033 TATTTTGTGG
Statistics
Matches: 428, Mismatches: 77, Indels: 24
0.81 0.15 0.05
Matches are distributed among these distances:
105 1 0.00
106 106 0.25
107 183 0.43
108 133 0.31
109 5 0.01
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (106 bp):
ATTTTACCCTATGGGGGTATTTCTGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCCTA
TGGGATATTTCGGTCATTCTACCCTATAGGGTATTTCGGTG
Found at i:29644322 original size:20 final size:19
Alignment explanation
Indices: 29644281--29644322 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
29644271 AGCCCAATGA
**
29644281 GCCCACATGGCCCATTTTG
1 GCCCACATGGCCCATTACG
29644300 GCCCACCATGGCCCATTACG
1 GCCCA-CATGGCCCATTACG
29644320 GCC
1 GCC
29644323 AAAGCCCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.19
Consensus pattern (19 bp):
GCCCACATGGCCCATTACG
Found at i:29651373 original size:41 final size:41
Alignment explanation
Indices: 29651315--29651420 Score: 185
Period size: 41 Copynumber: 2.6 Consensus size: 41
29651305 AATGAGATAA
* * *
29651315 TTCAGACTTTACATCTAGCAGGCTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
29651356 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
29651397 TTCAGACTTTACGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
29651421 AATTGCCAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
Found at i:29659176 original size:92 final size:92
Alignment explanation
Indices: 29659040--29659323 Score: 318
Period size: 92 Copynumber: 3.1 Consensus size: 92
29659030 CAATACGTCA
* * * * *
29659040 TGTTATCAAGGGAGAATATTTAGCCTACAAGCTTTTCACCATGTGTATCCAACATGTTATCGGTT
1 TGTTATCGAGGGAGAATATTTAGCCTACAAGCTTTACACTATGTGTATCTAACATGTTATCAGTT
*
29659105 GGAATAGCTCTTATTAGTAATCTAGCG
66 GGAATAGCTCTTATGAGTAATCTAGCG
* ** * * *
29659132 TGTTAT-TAGGAGAGAATATTTAGCCTACGGGCTTTACACTATGTGTATCTATCGTGTTATCATT
1 TGTTATCGAGG-GAGAATATTTAGCCTACAAGCTTTACACTATGTGTATCTAACATGTTATCAGT
* * * * *
29659196 TGGAATAGATGTTATGAGTAATTTGGCA
65 TGGAATAGCTCTTATGAGTAATCTAGCG
* ** * *
29659224 TGTTATCGAGGGAGAATATTTAGCCTACAAGCTTTGCACTATGTCAATCTAGCATGTTATTAGTT
1 TGTTATCGAGGGAGAATATTTAGCCTACAAGCTTTACACTATGTGTATCTAACATGTTATCAGTT
* * * *
29659289 GGAATAACTCTTATGAGCAAACTAACG
66 GGAATAGCTCTTATGAGTAATCTAGCG
29659316 TGTTATCG
1 TGTTATCG
29659324 GATGGTTACC
Statistics
Matches: 155, Mismatches: 35, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
91 3 0.02
92 149 0.96
93 3 0.02
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (92 bp):
TGTTATCGAGGGAGAATATTTAGCCTACAAGCTTTACACTATGTGTATCTAACATGTTATCAGTT
GGAATAGCTCTTATGAGTAATCTAGCG
Found at i:29663322 original size:27 final size:27
Alignment explanation
Indices: 29663289--29663361 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
29663279 CAAAAAGGTT
29663289 GTAAAATTACTGAAATACCCCCAAAGG
1 GTAAAATTACTGAAATACCCCCAAAGG
* * *
29663316 GTAAAATTA-TCGAAATACCCTCGATGG
1 GTAAAATTACT-GAAATACCCCCAAAGG
**
29663343 GTAAAATTACCAAAATACC
1 GTAAAATTACTGAAATACC
29663362 TTCGATGGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.22
Consensus pattern (27 bp):
GTAAAATTACTGAAATACCCCCAAAGG
Found at i:29663366 original size:27 final size:27
Alignment explanation
Indices: 29663314--29663403 Score: 119
Period size: 27 Copynumber: 3.3 Consensus size: 27
29663304 TACCCCCAAA
*
29663314 GGGTAAAATTATCGAAATACCCTCGAT
1 GGGTAAAATTATCGAAATACCTTCGAT
* *
29663341 GGGTAAAATTACCAAAATACCTTCGAT
1 GGGTAAAATTATCGAAATACCTTCGAT
* *
29663368 GGATAAAATTATCGAAATACCTCCG-T
1 GGGTAAAATTATCGAAATACCTTCGAT
29663394 AGGGTAAAAT
1 -GGGTAAAAT
29663404 AACTGTTATA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
26 1 0.02
27 53 0.98
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.26
Consensus pattern (27 bp):
GGGTAAAATTATCGAAATACCTTCGAT
Found at i:29667540 original size:182 final size:182
Alignment explanation
Indices: 29667229--29667583 Score: 665
Period size: 182 Copynumber: 2.0 Consensus size: 182
29667219 TTTGCATAAA
* *
29667229 TTTTAAGGAATCCTTAGTTAAATAGTGACATAGAAATATGCATATTTTTTTCTAAGTGACAAATC
1 TTTTAAGGAATCCTTAGTTAAACAGTGACATAGAAATATGCACATTTTTTTCTAAGTGACAAATC
*
29667294 TAAGATCTCGAAAGAGCTTATGATTTAGCTTCCAAGTTCATAAATGGTTGAGTTGCCATAGAATT
66 TAAGATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCATAGAATT
*
29667359 TTTCCTAGACATTGTTAAACATGATAAGGAATGAATTGAATTATGAACATTT
131 TTTCCAAGACATTGTTAAACATGATAAGGAATGAATTGAATTATGAACATTT
29667411 TTTTAAGGAATCCTTAGTTAAACAGTGACATAGAAATATGCACATTTTTTTCTAAGTGACAAATC
1 TTTTAAGGAATCCTTAGTTAAACAGTGACATAGAAATATGCACATTTTTTTCTAAGTGACAAATC
*
29667476 TAAGATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCGTAGAATT
66 TAAGATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCATAGAATT
29667541 TTTCCAAGACATTGTTAAACATGATAAGGAATGAATTGAATTA
131 TTTCCAAGACATTGTTAAACATGATAAGGAATGAATTGAATTA
29667584 AAAGTTGTAG
Statistics
Matches: 168, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
182 168 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (182 bp):
TTTTAAGGAATCCTTAGTTAAACAGTGACATAGAAATATGCACATTTTTTTCTAAGTGACAAATC
TAAGATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCATAGAATT
TTTCCAAGACATTGTTAAACATGATAAGGAATGAATTGAATTATGAACATTT
Found at i:29673465 original size:6 final size:6
Alignment explanation
Indices: 29673454--29673491 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
29673444 GCCTAAAAGG
*
29673454 AATTTT AATTTT AATTTT AATTTT CAATTCT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT -AATTTT AATTTT A
29673492 TGTTCAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (6 bp):
AATTTT
Found at i:29673487 original size:19 final size:18
Alignment explanation
Indices: 29673454--29673491 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
29673444 GCCTAAAAGG
*
29673454 AATTTTAATTTTAATTTT
1 AATTTTAATTCTAATTTT
29673472 AATTTTCAATTCTAATTTT
1 AATTTT-AATTCTAATTTT
29673491 A
1 A
29673492 TGTTCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTTAATTCTAATTTT
Found at i:29679038 original size:27 final size:27
Alignment explanation
Indices: 29679000--29679054 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
29678990 GAAAATCAAC
29679000 AAGCAAATAATGCATTAGATTTTTCTT
1 AAGCAAATAATGCATTAGATTTTTCTT
29679027 AAGCAAATAATGCATTAGATTTTTCTT
1 AAGCAAATAATGCATTAGATTTTTCTT
29679054 A
1 A
29679055 CCTTGTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (27 bp):
AAGCAAATAATGCATTAGATTTTTCTT
Found at i:29681780 original size:50 final size:50
Alignment explanation
Indices: 29681719--29681913 Score: 232
Period size: 50 Copynumber: 3.9 Consensus size: 50
29681709 ATGTTCGCTT
* * * *
29681719 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCTCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACATCCGGTA
* * *
29681769 CACGTAGTAGCCTGCACATAATACTACACACGTGATCGA-AACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAAC-ATCCGGTA
* * * *
29681820 CGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACA-TCCGGTA
* *
29681870 CACATAGTAGCCTGCACATAGTACTTCACACGTGACCATCACAT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACAT
29681914 TCACTTTTAC
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
49 1 0.01
50 78 0.65
51 41 0.34
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACATCCGGTA
Found at i:29681846 original size:101 final size:101
Alignment explanation
Indices: 29681721--29681904 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 101
29681711 GTTCGCTTCA
* * *
29681721 CATAGTAGCCTGCACATAGTACTACACATGTGACC-ATTACCTCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-CTCCGATACACATAGTAGCCTGCA
29681785 CATAATACTACACACGTGATCGAAACTATCCGGTACG
65 CATAATACTACACACGTGATCGAAACTATCCGGTACG
* *
29681822 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTACACATAGTAGCCTGCAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCACTCCGATACACATAGTAGCCTGCAC
* *
29681887 ATAGTACTTCACACGTGA
66 ATAATACTACACACGTGA
29681905 CCATCACATT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
101 72 0.96
102 3 0.04
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCACTCCGATACACATAGTAGCCTGCAC
ATAATACTACACACGTGATCGAAACTATCCGGTACG
Found at i:29684753 original size:42 final size:42
Alignment explanation
Indices: 29684673--29684754 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
29684663 CATTTTCTCT
* **
29684673 ATGCCATAGTCCAACTATGGTCTTAAACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTAAACATATGCACATATTG
* *
29684715 ATGCCATAGCCCAATTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTAAACA-TATGCACATAT
29684755 CACACCGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTAAACATATGCACATATTG
Found at i:29687595 original size:101 final size:101
Alignment explanation
Indices: 29687413--29687599 Score: 259
Period size: 101 Copynumber: 1.8 Consensus size: 101
29687403 ATGTTCGCTT
* * * * * *
29687413 CACATAATAGCTTGCACATAGTACTACACATGTGCCCATTACCATCTGATACACGTAGTAGTCTG
1 CACATAATAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTA
29687478 CACATAGTACTACACACGTGATTGAAACTATCTGGTA
65 CACATAGTACTACACACGTGATTGAAACTATCTGGTA
* * *
29687515 CACATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTA
1 CACATAATAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTA
*
29687579 CACATAGTACTCCACACGTGA
65 CACATAGTACTACACACGTGA
29687600 CCATCACATT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
100 4 0.05
101 37 0.50
102 33 0.45
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (101 bp):
CACATAATAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTAC
ACATAGTACTACACACGTGATTGAAACTATCTGGTA
Found at i:29696103 original size:12 final size:13
Alignment explanation
Indices: 29696083--29696114 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
29696073 AAGAACTTTA
29696083 TTATCTTCTATGT
1 TTATCTTCTATGT
29696096 TT-TCTTCTATGT
1 TTATCTTCTATGT
29696108 TTATCTT
1 TTATCTT
29696115 GTTTGCTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.12, C:0.16, G:0.06, T:0.66
Consensus pattern (13 bp):
TTATCTTCTATGT
Found at i:29697150 original size:39 final size:39
Alignment explanation
Indices: 29697107--29697186 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
29697097 TCATAATTTA
*
29697107 TCCTGGTTTAGAAAGTGAGGTTGAAAGATAGGTGAGTAT
1 TCCTGGTTTAGAAAGCGAGGTTGAAAGATAGGTGAGTAT
29697146 TCCTGGTTTAGAAAGCGAGGTTGAAAGATAGGTGAGTAT
1 TCCTGGTTTAGAAAGCGAGGTTGAAAGATAGGTGAGTAT
29697185 TC
1 TC
29697187 ATTGATTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (39 bp):
TCCTGGTTTAGAAAGCGAGGTTGAAAGATAGGTGAGTAT
Found at i:29700488 original size:27 final size:27
Alignment explanation
Indices: 29700457--29700519 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
29700447 TTAGAGTGTG
29700457 CCACAAAGGCATTC-CCTTCATAGATCA
1 CCACAAAGGC-TTCACCTTCATAGATCA
* **
29700484 CCACAAATGCTTCATTTTTCATAGATCA
1 CCACAAAGGCTTCA-CCTTCATAGATCA
29700512 CCACAAAG
1 CCACAAAG
29700520 ACATCCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 3 0.10
27 9 0.30
28 18 0.60
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (27 bp):
CCACAAAGGCTTCACCTTCATAGATCA
Found at i:29702677 original size:8 final size:8
Alignment explanation
Indices: 29702666--29702692 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
29702656 TTTTTCTACT
29702666 TTTGTGAC
1 TTTGTGAC
29702674 TTTGTGAC
1 TTTGTGAC
29702682 TTTGTGAC
1 TTTGTGAC
29702690 TTT
1 TTT
29702693 TTCATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.56
Consensus pattern (8 bp):
TTTGTGAC
Found at i:29704036 original size:101 final size:102
Alignment explanation
Indices: 29703966--29704149 Score: 255
Period size: 102 Copynumber: 1.8 Consensus size: 102
29703956 GATGGTCACG
*
29703966 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGTACAAT
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGTACAAT
* * * *
29704029 GTGTAGGCTACTATGCGTACCAGATAGCTTCGATAACA
65 GTGTAGGCTACTATGTGAAACAGAAAGCTTCGATAACA
* * * *
29704067 TGTGTAGTACTATGTTTAGGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTACTATG
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTACAATG
*
29704132 TGCAGGCTACTATGTGAA
66 TGTAGGCTACTATGTGAA
29704150 CCGGTATCAT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
101 34 0.47
102 35 0.48
103 4 0.05
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (102 bp):
TGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTACAATG
TGTAGGCTACTATGTGAAACAGAAAGCTTCGATAACA
Found at i:29704090 original size:51 final size:49
Alignment explanation
Indices: 29703958--29704143 Score: 203
Period size: 51 Copynumber: 3.7 Consensus size: 49
29703948 GTGAAAGTGA
*
29703958 TGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-ATGAT
1 TGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGATA-G-T
* * * * *
29704008 AGGTCGCATGTGTAGTACAATGTGTAGGCTACTATGCGTACCAGATAGCT
1 TGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGATAG-T
* * * * *
29704058 TCGATAACATGTGTAGTACTATGTTTAGGCTACTACGTGTATCGGATAGT
1 T-GGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGATAGT
*
29704108 GATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 --TGGTCACATGTGTAGTACTATGTGTAGGCTACTA
29704144 TGTGAACCGG
Statistics
Matches: 111, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
50 42 0.38
51 68 0.61
52 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (49 bp):
TGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGATAGT
Found at i:29704393 original size:16 final size:16
Alignment explanation
Indices: 29704372--29704403 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29704362 TGATTGAAAG
*
29704372 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
29704388 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
29704404 GCGACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:29712694 original size:16 final size:16
Alignment explanation
Indices: 29712673--29712703 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29712663 GTTATTATGA
29712673 TTGATTAAAAAACAAC
1 TTGATTAAAAAACAAC
29712689 TTGATTAAAAAACAA
1 TTGATTAAAAAACAA
29712704 GTATTTGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (16 bp):
TTGATTAAAAAACAAC
Found at i:29715913 original size:91 final size:91
Alignment explanation
Indices: 29715799--29716096 Score: 542
Period size: 91 Copynumber: 3.3 Consensus size: 91
29715789 TTGATTTTAG
* *
29715799 TAAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
29715864 TTTGATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
29715890 TAAATTCATATAAGAAAATTTATTACCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
29715955 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
29715981 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
29716046 TTTAAAATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
29716072 GAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
29716097 GTAATAATTA
Statistics
Matches: 200, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 200 1.00
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:29716049 original size:47 final size:47
Alignment explanation
Indices: 29715814--29716049 Score: 210
Period size: 47 Copynumber: 5.1 Consensus size: 47
29715804 TCATATAAGA
29715814 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
** *
29715861 ATATTTGA-TATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTT-ATTATTAAGAATTTTATGAAATTATATATCATT-AT-TAA-ATT
* **
29715905 AAATTTATTACCAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
* ** *
29715952 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATT-AT-TAA-ATT
* *
29715996 AAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
29716043 ATATTTA
1 ATATTTA
29716050 AAATTAATTA
Statistics
Matches: 146, Mismatches: 23, Indels: 40
0.70 0.11 0.19
Matches are distributed among these distances:
43 7 0.05
44 46 0.32
45 16 0.11
46 16 0.11
47 54 0.37
48 7 0.05
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (47 bp):
ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
Found at i:29716188 original size:59 final size:58
Alignment explanation
Indices: 29716123--29716431 Score: 197
Period size: 59 Copynumber: 5.2 Consensus size: 58
29716113 ATTTTATTAA
29716123 ATCATATATTTTAATTAAAATATATTTAATAATAATTGTTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAATAATTGTTT-AAATTATATTTTATAGT
* * * * * * * *
29716182 GTCATATATTATGAGTTTAGTAAAT-TCATATAAGAATTA-TGATT--ATTAAGAATTTTATTA-
1 ATCATATATT-TTA-ATTA--AAATAT-ATTTAATAATAATTGTTTAAATT-A-TATTTTA-TAG
*
29716242 A
58 T
*
29716243 ATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAATAATTGTTT-AAATTATATTTTATAGT
* * ** * * *
29716302 ATCATATATTATGATTTTAGTAAAT-TCATAAAAGAAT-ATTGATT--ATTAAGAATTTTATTA-
1 ATCATATATT-TTA-ATTA--AAATAT-ATTTAATAATAATTGTTTAAATT-A-TATTTTA-TAG
*
29716362 A
58 T
* *
29716363 ATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAATAATTGT-TTAAATTATATTTTATAGT
29716422 ATCATATATT
1 ATCATATATT
29716432 ATGATTTGAG
Statistics
Matches: 183, Mismatches: 39, Indels: 56
0.66 0.14 0.20
Matches are distributed among these distances:
57 24 0.13
58 12 0.07
59 54 0.30
60 12 0.07
61 42 0.23
62 15 0.08
63 24 0.13
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (58 bp):
ATCATATATTTTAATTAAAATATATTTAATAATAATTGTTTAAATTATATTTTATAGT
Found at i:29716237 original size:120 final size:119
Alignment explanation
Indices: 29716112--29716520 Score: 705
Period size: 120 Copynumber: 3.4 Consensus size: 119
29716102 AATTATTTTA
*
29716112 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTGTTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
29716177 ATAGTGTCATATATTATGAGTTTAGTAAATTCATATAAGAAT-TATGATTATTAAG
66 ATAGTATCATATATTATGA-TTTAGTAAATTCATATAAGAATAT-TGATTATTAAG
29716232 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
29716297 ATAGTATCATATATTATGATTTTAGTAAATTCATAAAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGA-TTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
29716352 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTT
29716416 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
65 TATAGTATCATATATTATGATTT-AGTAAATTCATATAAGAATATTGATTATTAAG
* *
29716472 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTA
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTA
29716521 CGTTAAAATA
Statistics
Matches: 279, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
119 3 0.01
120 273 0.98
121 3 0.01
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (119 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATATATTATGATTTAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:29716381 original size:18 final size:17
Alignment explanation
Indices: 29716353--29716387 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29716343 ATTATTAAGA
*
29716353 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29716370 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29716388 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29716512 original size:15 final size:15
Alignment explanation
Indices: 29716477--29716518 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29716467 TTAAGAATTT
*
29716477 TATTAAATTAT-ATA
1 TATTTAATTATAATA
29716491 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
29716505 TATTTAATAATAAT
1 TATTTAATTATAAT
29716519 TACGTTAAAA
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:29716731 original size:16 final size:16
Alignment explanation
Indices: 29716707--29716739 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29716697 TTGATTTGCT
*
29716707 ATTATGCCTCTATTCC
1 ATTACGCCTCTATTCC
29716723 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
29716739 A
1 A
29716740 ATACAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:29740825 original size:30 final size:30
Alignment explanation
Indices: 29740782--29740853 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
29740772 TAACACATCT
* * * *
29740782 CTTTTCTTTATTCGATAGCCGAGGCTATCC
1 CTTTTCATAATTCGATAGCCAAAGCTATCC
* *
29740812 CTTTTCGTAATTCGATAGTCAAAGCTATCC
1 CTTTTCATAATTCGATAGCCAAAGCTATCC
*
29740842 TTTTTCATAATT
1 CTTTTCATAATT
29740854 TGATGGTTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (30 bp):
CTTTTCATAATTCGATAGCCAAAGCTATCC
Found at i:29740872 original size:30 final size:30
Alignment explanation
Indices: 29740838--29740917 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 30
29740828 AGTCAAAGCT
* **
29740838 ATCCTTTTTCATAATTTGATGGTTGTCACC
1 ATCCTTTTTCATAATTTGATGATCATCACC
* ** *
29740868 ATCCTATTTCATGGTTTGATGATCATCAGC
1 ATCCTTTTTCATAATTTGATGATCATCACC
*
29740898 ATCCCTTTTCATAATTTGAT
1 ATCCTTTTTCATAATTTGAT
29740918 AGCCGAAGTC
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.45
Consensus pattern (30 bp):
ATCCTTTTTCATAATTTGATGATCATCACC
Found at i:29740960 original size:29 final size:30
Alignment explanation
Indices: 29740897--29740969 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
29740887 TGATCATCAG
*
29740897 CATCCCTTTTCATAATTTGATAGCCGAAGT
1 CATCCCTTTTCATAATTCGATAGCCGAAGT
*
29740927 CATCCCTTTTCATGA-TCGATAGCCGAAG-
1 CATCCCTTTTCATAATTCGATAGCCGAAGT
29740955 CTATCCCTTTTCATA
1 C-ATCCCTTTTCATA
29740970 GTTCAATGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 24 0.62
30 14 0.36
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.36
Consensus pattern (30 bp):
CATCCCTTTTCATAATTCGATAGCCGAAGT
Found at i:29740995 original size:29 final size:29
Alignment explanation
Indices: 29740957--29741030 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
29740947 AGCCGAAGCT
*
29740957 ATCCCTTTTCATAGTTCAATGGTCATCACC
1 ATCCCTTTTCATAATT-AATGGTCATCACC
* * **
29740987 ATCCCTTTCCATAATTTATGGTTGTCACC
1 ATCCCTTTTCATAATTAATGGTCATCACC
29741016 ATCCCTTTTCATAAT
1 ATCCCTTTTCATAAT
29741031 CGATAGACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
29 24 0.63
30 14 0.37
ACGTcount: A:0.23, C:0.28, G:0.08, T:0.41
Consensus pattern (29 bp):
ATCCCTTTTCATAATTAATGGTCATCACC
Found at i:29762048 original size:20 final size:21
Alignment explanation
Indices: 29762020--29762058 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
29762010 TGTAAACTTA
29762020 AGTGCTTAAATT-ATATTTTT
1 AGTGCTTAAATTGATATTTTT
*
29762040 AGTGGTTAAATTGATATTT
1 AGTGCTTAAATTGATATTT
29762059 AGGCTTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (21 bp):
AGTGCTTAAATTGATATTTTT
Found at i:29765698 original size:28 final size:28
Alignment explanation
Indices: 29765658--29765800 Score: 135
Period size: 28 Copynumber: 5.1 Consensus size: 28
29765648 AGGCATTCCC
* *
29765658 TTCATAGATTGCCATAAATGCTTCTTTT
1 TTCATAGATTGCCATAAAGGCTTCCTTT
*
29765686 TTCATAGATTGCCATAAAGGCTTCCATT
1 TTCATAGATTGCCATAAAGGCTTCCTTT
* *
29765714 TTCATAAATCT-CCACAAAGGCTTCCTTT
1 TTCATAGAT-TGCCATAAAGGCTTCCTTT
* *** *
29765742 TTCATAAACCACCACAAAGGCTTCCTTT
1 TTCATAGATTGCCATAAAGGCTTCCTTT
* * * *
29765770 TTAAGAGATCGCCATGAAGGCTTCCTCTT
1 TTCATAGATTGCCATAAAGGCTTCCT-TT
29765799 TT
1 TT
29765801 GGCGTTTTTA
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
28 92 0.95
29 5 0.05
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (28 bp):
TTCATAGATTGCCATAAAGGCTTCCTTT
Found at i:29768938 original size:22 final size:21
Alignment explanation
Indices: 29768913--29768961 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
29768903 AAGTCATGTA
29768913 ATTTATCAAACCCAATAA-ATAT
1 ATTTATCAAACCCAA-AATAT-T
* *
29768935 ATTTATTATACCCAAAATATT
1 ATTTATCAAACCCAAAATATT
29768956 ATTTAT
1 ATTTAT
29768962 TTAATTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTATCAAACCCAAAATATT
Found at i:29775535 original size:24 final size:24
Alignment explanation
Indices: 29775496--29775593 Score: 88
Period size: 24 Copynumber: 3.9 Consensus size: 24
29775486 TTAGTTTATC
* * *
29775496 TAATATAAATTCACCATAATCAAT
1 TAATATATATTAACCATAATTAAT
*
29775520 TAATATATATTAACCATAATTAGT
1 TAATATATATTAACCATAATTAAT
* *
29775544 TCACATAATATAATTAATCATAATTACT
1 T-A-AT-ATAT-ATTAACCATAATTAAT
* *
29775572 TAATATATATTTACTATAATTA
1 TAATATATATTAACCATAATTA
29775594 GTTTACATAT
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
24 32 0.52
25 5 0.08
26 4 0.07
27 5 0.08
28 15 0.25
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (24 bp):
TAATATATATTAACCATAATTAAT
Found at i:29775565 original size:28 final size:27
Alignment explanation
Indices: 29775520--29775602 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 27
29775510 CATAATCAAT
*
29775520 TAATATATATTAACCATAATTAGTTCACA
1 TAATATA-ATTAATCATAATTAGTT-ACA
*
29775549 TAATATAATTAATCATAATTACTTA-A
1 TAATATAATTAATCATAATTAGTTACA
* *
29775575 T-ATATATTTACT-ATAATTAGTTTACA
1 TAATATAATTAATCATAATTAG-TTACA
29775601 TA
1 TA
29775603 TTTACAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
24 7 0.15
25 12 0.26
26 4 0.09
27 1 0.02
28 15 0.33
29 7 0.15
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (27 bp):
TAATATAATTAATCATAATTAGTTACA
Found at i:29775591 original size:52 final size:53
Alignment explanation
Indices: 29775459--29775602 Score: 168
Period size: 52 Copynumber: 2.7 Consensus size: 53
29775449 AGTAAACAAT
* * *
29775459 TAATTACTTGATACAGT-TTTACCATAATTAGTTTATC-TAATATAAATTCACCA
1 TAATTACTTAATATA-TATTTACCATAATTAGTTTA-CATAATATAAATTAACCA
* * * * *
29775512 TAATCAATTAATATATATTAACCATAATTAGTTCACATAATAT-AATTAATCA
1 TAATTACTTAATATATATTTACCATAATTAGTTTACATAATATAAATTAACCA
*
29775564 TAATTACTTAATATATATTTACTATAATTAGTTTACATA
1 TAATTACTTAATATATATTTACCATAATTAGTTTACATA
29775603 TTTACAATAA
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
52 43 0.57
53 33 0.43
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (53 bp):
TAATTACTTAATATATATTTACCATAATTAGTTTACATAATATAAATTAACCA
Found at i:29775603 original size:24 final size:24
Alignment explanation
Indices: 29775519--29775603 Score: 62
Period size: 24 Copynumber: 3.4 Consensus size: 24
29775509 CCATAATCAA
* * *
29775519 TTAATATATATTAACCATAATTAG
1 TTAACATATATTTACTATAATTAG
* * *
29775543 TTCACATAATATAATTAATCATAATTAC
1 TTAACAT-ATAT--TTACT-ATAATTAG
*
29775571 TTAATATATATTTACTATAATTAG
1 TTAACATATATTTACTATAATTAG
*
29775595 TTTACATAT
1 TTAACATAT
29775604 TTACAATAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
24 19 0.42
25 8 0.18
27 6 0.13
28 12 0.27
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (24 bp):
TTAACATATATTTACTATAATTAG
Found at i:29781006 original size:22 final size:22
Alignment explanation
Indices: 29780962--29781020 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
29780952 ATGAATGTTG
*
29780962 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATATAATTAT
29780986 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATATAATTAT
*
29781008 TTTAAGTTT-TCAT
1 TTTAAATTTATCAT
29781021 GTATCATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.55
24 11 0.33
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATCATATAATTAT
Found at i:29786146 original size:10 final size:10
Alignment explanation
Indices: 29786131--29786187 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 10
29786121 CAGATCCAAT
29786131 TCAAAAAAAA
1 TCAAAAAAAA
29786141 TCAAAAAAAA
1 TCAAAAAAAA
29786151 T-AAAAAAAA
1 TCAAAAAAAA
29786160 -CAAAAAAGAA
1 TCAAAAAA-AA
*
29786170 TAAAAAGAAAAA
1 T-CAAA-AAAAA
29786182 TCAAAA
1 TCAAAA
29786188 TCAAGGTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 14 0.35
10 14 0.35
11 3 0.08
12 6 0.15
13 3 0.08
ACGTcount: A:0.81, C:0.07, G:0.04, T:0.09
Consensus pattern (10 bp):
TCAAAAAAAA
Found at i:29786157 original size:19 final size:19
Alignment explanation
Indices: 29786133--29786175 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
29786123 GATCCAATTC
29786133 AAAAAAAATCAAAAAA-AAT
1 AAAAAAAA-CAAAAAAGAAT
29786152 AAAAAAAACAAAAAAGAAT
1 AAAAAAAACAAAAAAGAAT
29786171 AAAAA
1 AAAAA
29786176 GAAAAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.86, C:0.05, G:0.02, T:0.07
Consensus pattern (19 bp):
AAAAAAAACAAAAAAGAAT
Found at i:29786178 original size:9 final size:9
Alignment explanation
Indices: 29786133--29786175 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 9
29786123 GATCCAATTC
29786133 AAAAAAAAT
1 AAAAAAAAT
29786142 CAAAAAAAAT
1 -AAAAAAAAT
*
29786152 AAAAAAAAC
1 AAAAAAAAT
29786161 AAAAAAGAAT
1 AAAAAA-AAT
29786171 AAAAA
1 AAAAA
29786176 GAAAAATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 14 0.47
10 16 0.53
ACGTcount: A:0.86, C:0.05, G:0.02, T:0.07
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:29788510 original size:87 final size:88
Alignment explanation
Indices: 29788393--29788620 Score: 257
Period size: 88 Copynumber: 2.6 Consensus size: 88
29788383 AGATCAGTGA
* * * * *
29788393 AGATCGAAA-ACA-AAGCCTTGCCTCCATCGGTTGCAGTGGAGCAGGTTAAAGATAGCGGATCTT
1 AGATC-AAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAACAGATCTC
* * *
29788456 GCCTTCCTAAG-C-AGTAGTGGAGC
65 ACCTTCCTAAGTCGA-TAGCGAAGC
* * *
29788479 AGATCGAAGATACCAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAACAGATCTCA
1 AGATCAAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAACAGATCTCA
** *
29788544 CCTTCCTCCGTCGATGGCGAAGC
66 CCTTCCTAAGTCGATAGCGAAGC
* * *
29788567 AGATCAAAGGCACAAGCCTTGCCTCCCTCGGTTGTAGTGGAACAGGTTGAAGAT
1 AGATCAAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGAT
29788621 TTGAAACTAC
Statistics
Matches: 118, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
85 2 0.02
86 7 0.06
87 53 0.45
88 55 0.47
89 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (88 bp):
AGATCAAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAACAGATCTCA
CCTTCCTAAGTCGATAGCGAAGC
Found at i:29788518 original size:43 final size:43
Alignment explanation
Indices: 29788406--29788533 Score: 130
Period size: 43 Copynumber: 3.0 Consensus size: 43
29788396 TCGAAAACAA
* * *
29788406 AGCCTTGCCTCCATCGGTTGCAGTGGAGCAGGTTAAAGATAGC
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATACC
* * * ** ** * * *
29788449 GGATCTTGCCTTCCTAAGCAGTAGTGGAGCAGATCGAAGATACC
1 AG-CCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATACC
29788493 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATA
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATA
29788534 ACAGATCTCA
Statistics
Matches: 61, Mismatches: 23, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
43 31 0.51
44 30 0.49
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (43 bp):
AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATACC
Found at i:29788774 original size:131 final size:131
Alignment explanation
Indices: 29788623--29789080 Score: 704
Period size: 131 Copynumber: 3.5 Consensus size: 131
29788613 TTGAAGATTT
*
29788623 GAAACTACAGATCTTATCTCCCTAAGTAATAGTGGAGCAAATCGAAGACGACGAATCTTATCTTC
1 GAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAAATCGAAGACGACGAATCTTATCTTC
*
29788688 CCCAGGAGTAGGGAAACATATTTAAGCCACAAGTCCTATTTCCCTGAGCAGCAGGGGAATAGGTT
66 CCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGAGCAGCAGGGGAATAGGTT
*
29788753 A
131 G
* *
29788754 GAAACTATAGATCTTATCTCCCTAAGCAATAGTGGAGCAAATCGAAGAC-AGTGAATCTTATCTT
1 GAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAAATCGAAGACGA-CGAATCTTATCTT
*
29788818 CCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGAGCAGCAAGGGAATAGGT
65 CCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGAGCAGCAGGGGAATAGGT
29788883 TG
130 TG
* * *
29788885 GAAGCTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTC
1 GAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAAATCGAAGACGACGAATCTTATCTTC
* * * * *
29788950 CCGAAGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTG-GTCAGCAGTGGAGTAGGT
66 CCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGAG-CAGCAGGGGAATAGGT
29789014 TG
130 TG
* * * * **
29789016 GAAATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTC
1 GAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAAATCGAAGACGACGAATCTTATCTTC
29789081 AAGTGTAAGG
Statistics
Matches: 302, Mismatches: 22, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
130 2 0.01
131 300 0.99
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (131 bp):
GAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAAATCGAAGACGACGAATCTTATCTTC
CCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGAGCAGCAGGGGAATAGGTT
G
Found at i:29789335 original size:50 final size:50
Alignment explanation
Indices: 29789278--29789435 Score: 167
Period size: 50 Copynumber: 3.2 Consensus size: 50
29789268 CGAAGAATTT
* *
29789278 TGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAACCACATCGG
1 TGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAACGG
* ** * * **
29789328 TGAATCTTACTTCCCC-GAC-ATTGCAGTTAAAAAGATTAAAGCTACAACAA
1 TGAATCTTAC-TCCCCAGGCGA-TGCAGTGGAACAGATTAAAGCCACAACGG
* * * *
29789378 TGAATCTTACTTCTCAAGCGGTGCAGTGGAACAGATTAAAGCCACAACGG
1 TGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAACGG
29789428 TGAATCTT
1 TGAATCTT
29789436 GCTTCCTCGA
Statistics
Matches: 84, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
49 4 0.05
50 75 0.89
51 5 0.06
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (50 bp):
TGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAACGG
Found at i:29789451 original size:100 final size:100
Alignment explanation
Indices: 29789278--29789468 Score: 301
Period size: 100 Copynumber: 1.9 Consensus size: 100
29789268 CGAAGAATTT
* *
29789278 TGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAACCACATCGGTGAATCTTACTTCCC
1 TGAATCTTACTCCCCAAGCGATGCAGTGGAACAGATTAAAACCACAACGGTGAATCTTACTTCCC
29789343 CGACATTGCAGTTAAAAAGATTAAAGCTACAACAA
66 CGACATTGCAGTTAAAAAGATTAAAGCTACAACAA
* * * * * *
29789378 TGAATCTTACTTCTCAAGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCT
1 TGAATCTTACTCCCCAAGCGATGCAGTGGAACAGATTAAAACCACAACGGTGAATCTTACTTCCC
*
29789443 CGACATTGCAGTTAAACAGATTAAAG
66 CGACATTGCAGTTAAAAAGATTAAAG
29789469 TTACGAGTTA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 82 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (100 bp):
TGAATCTTACTCCCCAAGCGATGCAGTGGAACAGATTAAAACCACAACGGTGAATCTTACTTCCC
CGACATTGCAGTTAAAAAGATTAAAGCTACAACAA
Found at i:29789453 original size:50 final size:50
Alignment explanation
Indices: 29789299--29789468 Score: 189
Period size: 50 Copynumber: 3.4 Consensus size: 50
29789289 CCCCAGGCGA
* * * *
29789299 TGCAGTGGAACAGATTAAAACCACATCGGTGAATCTTACTTCCCCGACAT
1 TGCAGTGAAACAGATTAAAGCCACAACGGTGAATCTTACTTCCTCGACAT
* * * ** * **
29789349 TGCAGTTAAAAAGATTAAAGCTACAACAATGAATCTTACTT-CTCAAGCGG
1 TGCAGTGAAACAGATTAAAGCCACAACGGTGAATCTTACTTCCTCGA-CAT
* *
29789399 TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCTCGACAT
1 TGCAGTGAAACAGATTAAAGCCACAACGGTGAATCTTACTTCCTCGACAT
*
29789449 TGCAGTTAAACAGATTAAAG
1 TGCAGTGAAACAGATTAAAG
29789469 TTACGAGTTA
Statistics
Matches: 94, Mismatches: 24, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
49 3 0.03
50 87 0.93
51 4 0.04
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (50 bp):
TGCAGTGAAACAGATTAAAGCCACAACGGTGAATCTTACTTCCTCGACAT
Found at i:29790101 original size:11 final size:11
Alignment explanation
Indices: 29790077--29790112 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
29790067 TACTCGTTGT
29790077 TTTTTATTTT-
1 TTTTTATTTTA
29790087 TTTTTATTTTA
1 TTTTTATTTTA
29790098 TTTTTATTTTA
1 TTTTTATTTTA
29790109 TTTT
1 TTTT
29790113 ACGAATCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:29790113 original size:5 final size:5
Alignment explanation
Indices: 29790078--29790113 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
29790068 ACTCGTTGTT
*
29790078 TTTTA TTTTT TTTTA TTTTA TTTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA
29790114 CGAATCTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:29790987 original size:22 final size:22
Alignment explanation
Indices: 29790943--29791001 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
29790933 ATGAATGTTG
*
29790943 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATATAATTAT
29790967 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATATAATTAT
*
29790989 TTTAAGTTT-TCAT
1 TTTAAATTTATCAT
29791002 GTATCATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.55
24 11 0.33
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATCATATAATTAT
Found at i:29795037 original size:20 final size:19
Alignment explanation
Indices: 29795008--29795052 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
29794998 AAATCAAAAG
29795008 AAAAACCCGGAACCCCGAA
1 AAAAACCCGGAACCCCGAA
29795027 AAAATACCCGGAACCCCGAA
1 AAAA-ACCCGGAACCCCGAA
29795047 AGAAAA
1 A-AAAA
29795053 ACCCTTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.17
20 17 0.71
21 3 0.12
ACGTcount: A:0.51, C:0.31, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAACCCGGAACCCCGAA
Found at i:29815788 original size:15 final size:15
Alignment explanation
Indices: 29815745--29815788 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
29815735 TTCTATTCAG
*
29815745 TATTAAAACTTTTTT
1 TATTAAAGCTTTTTT
*
29815760 TATT--AGCTCTTTT
1 TATTAAAGCTTTTTT
29815773 TATTAAAGCTTTTTT
1 TATTAAAGCTTTTTT
29815788 T
1 T
29815789 TTTCAAGGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 11 0.46
15 13 0.54
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.61
Consensus pattern (15 bp):
TATTAAAGCTTTTTT
Found at i:29818642 original size:24 final size:25
Alignment explanation
Indices: 29818590--29818650 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 25
29818580 ATACATGTAT
* * *
29818590 GCTCATACGAGCTTTGAATCGGTAT
1 GCTCATACGAGCTGTGAAACGGTAA
*
29818615 GCTCTTACGAGCTGT-AAACGGTAA
1 GCTCATACGAGCTGTGAAACGGTAA
*
29818639 GCTCATATGAGC
1 GCTCATACGAGC
29818651 CAAATATTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 17 0.57
25 13 0.43
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (25 bp):
GCTCATACGAGCTGTGAAACGGTAA
Found at i:29818681 original size:25 final size:25
Alignment explanation
Indices: 29818633--29818692 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
29818623 GAGCTGTAAA
*
29818633 CGGTAAGCTCATATGAGCCAAATAT
1 CGGTAAGCTCATACGAGCCAAATAT
* **
29818658 TGGTAAGCTCATACGAGCTGAATAT
1 CGGTAAGCTCATACGAGCCAAATAT
*
29818683 CAGTAAGCTC
1 CGGTAAGCTC
29818693 TCTCGAGTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (25 bp):
CGGTAAGCTCATACGAGCCAAATAT
Found at i:29819539 original size:11 final size:11
Alignment explanation
Indices: 29819523--29819552 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29819513 CTAAATGATA
*
29819523 TTTTAATTTGG
1 TTTTAATTCGG
29819534 TTTTAATTCGG
1 TTTTAATTCGG
29819545 TTTTAATT
1 TTTTAATT
29819553 ACCTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.13, T:0.63
Consensus pattern (11 bp):
TTTTAATTCGG
Found at i:29821775 original size:8 final size:8
Alignment explanation
Indices: 29821762--29821793 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
29821752 CAATTAGTAT
29821762 CATTTAAC
1 CATTTAAC
29821770 CATTTAAC
1 CATTTAAC
29821778 CATTTAAC
1 CATTTAAC
29821786 CATTTAAC
1 CATTTAAC
29821794 TTTCATATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.38
Consensus pattern (8 bp):
CATTTAAC
Found at i:29822229 original size:16 final size:17
Alignment explanation
Indices: 29822208--29822241 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
29822198 GCATACAAGC
29822208 ATACATATAATTC-CAT
1 ATACATATAATTCACAT
29822224 ATACATATAATTCACAT
1 ATACATATAATTCACAT
29822241 A
1 A
29822242 ATTCATTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (17 bp):
ATACATATAATTCACAT
Found at i:29823428 original size:258 final size:260
Alignment explanation
Indices: 29822967--29823486 Score: 830
Period size: 258 Copynumber: 2.0 Consensus size: 260
29822957 AAACCATAAA
*
29822967 TAATTAAAAATTATAAACCAAAACCAATAGAGACTGATTAATACTTATTAAAAATAGTCCGAGGT
1 TAATTAAAAATTATAAACCAAAACCAATAGAGACTGATTAATACTTATTAAAAATAGTCCGAAGT
* * * * *
29823032 CAAAGGTGATTCTCCGTATGTCGAGTCTGGCCCTAGTTTCGAGCTTTACTTGTAAAGTTAAACAC
66 CAAAGGTAATTCTCCGTATGTCGAGTCCGGCCCTAGTTTCAAGCTTTACCTGAAAAGTTAAACAC
* * *
29823097 TATGGGGGGTGAGCTTATGAAAGCTCAGTGTGAGTCGAACATTTATTTAAACACCCATAAATAGA
131 TATGGGGGGTGAGCTTATGAAAGCTCAATGTGAGTCAAACAATTATTTAAACACCCATAAATAGA
* * *
29823162 AGATATAGTTAAGCATATTACCGTTAACAAAAGAACACAGACCCATCATTGGAATTTCATATCAT
196 AAATATAGTGAAGCATATTACCATTAACAAAAGAACACAGACCCATCATTGGAATTTCATATCAT
*
29823227 TAATTAAAAATTATAAACCAAAACCAATAGAGATTGATTAATACTT-TTAAAAATAGTCCGAAGT
1 TAATTAAAAATTATAAACCAAAACCAATAGAGACTGATTAATACTTATTAAAAATAGTCCGAAGT
* * ** *
29823291 CCAGGGTAATTCTCCGTAT-TCCGAGTCCGGTTCTAGTTTCAAGGTTTACCTGAAAAGTTAAACA
66 CAAAGGTAATTCTCCGTATGT-CGAGTCCGGCCCTAGTTTCAAGCTTTACCTGAAAAGTTAAACA
29823355 CTAT-GGGGGTGAGCTTATGAAAGCTCAATGTGAGTCAAACAATTATTTAAACACCCATAAATAG
130 CTATGGGGGGTGAGCTTATGAAAGCTCAATGTGAGTCAAACAATTATTTAAACACCCATAAATAG
* *
29823419 AAAATATAGTGAAGCATATTAGCATTAACAGAAGAACACAGACCCATCATTGGAATTTCATATCA
195 AAAATATAGTGAAGCATATTACCATTAACAAAAGAACACAGACCCATCATTGGAATTTCATATCA
29823484 T
260 T
29823485 TA
1 TA
29823487 CATAGTAATT
Statistics
Matches: 239, Mismatches: 20, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
258 121 0.51
259 73 0.31
260 45 0.19
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (260 bp):
TAATTAAAAATTATAAACCAAAACCAATAGAGACTGATTAATACTTATTAAAAATAGTCCGAAGT
CAAAGGTAATTCTCCGTATGTCGAGTCCGGCCCTAGTTTCAAGCTTTACCTGAAAAGTTAAACAC
TATGGGGGGTGAGCTTATGAAAGCTCAATGTGAGTCAAACAATTATTTAAACACCCATAAATAGA
AAATATAGTGAAGCATATTACCATTAACAAAAGAACACAGACCCATCATTGGAATTTCATATCAT
Found at i:29823584 original size:5 final size:5
Alignment explanation
Indices: 29823574--29823617 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
29823564 GATAACATTT
*
29823574 AATAC AATAC AATAC AATAC AATAT AATAC AATAC AATAC AATA
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATA
29823618 TGTAGCATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (5 bp):
AATAC
Found at i:29823787 original size:28 final size:27
Alignment explanation
Indices: 29823755--29823835 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
29823745 ACTTGATGTG
*
29823755 GTAAAACTACCTAATAAAAAATAATGCA
1 GTAAAACTACCGAAT-AAAAATAATGCA
*
29823783 GTAAAACTACCGAATAAAAATAATGTA
1 GTAAAACTACCGAATAAAAATAATGCA
* *
29823810 GTAAAA-TGCTGAATAACAAATAATGC
1 GTAAAACTACCGAATAA-AAATAATGC
29823836 GATATAATCG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
26 8 0.17
27 25 0.53
28 14 0.30
ACGTcount: A:0.54, C:0.12, G:0.11, T:0.22
Consensus pattern (27 bp):
GTAAAACTACCGAATAAAAATAATGCA
Found at i:29824879 original size:10 final size:10
Alignment explanation
Indices: 29824868--29824901 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
29824858 TATTTCATTT
*
29824868 CAATTCAATT
1 CAATTCAATC
29824878 CAATTCAATC
1 CAATTCAATC
*
29824888 CAATCCAATC
1 CAATTCAATC
29824898 CAAT
1 CAAT
29824902 CCATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.29, G:0.00, T:0.29
Consensus pattern (10 bp):
CAATTCAATC
Found at i:29824884 original size:15 final size:15
Alignment explanation
Indices: 29824861--29824904 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29824851 ATGCATTTAT
* *
29824861 TTCATTTCAATTCAA
1 TTCAATTCAATCCAA
29824876 TTCAATTCAATCCAA
1 TTCAATTCAATCCAA
* *
29824891 TCCAATCCAATCCA
1 TTCAATTCAATCCA
29824905 TATATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (15 bp):
TTCAATTCAATCCAA
Found at i:29827879 original size:17 final size:18
Alignment explanation
Indices: 29827857--29827895 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29827847 GTTTTACAAT
29827857 AAAATAAA-TAAACATGC
1 AAAATAAAGTAAACATGC
* *
29827874 AAAATAAAGTGAACATGG
1 AAAATAAAGTAAACATGC
29827892 AAAA
1 AAAA
29827896 CTAATGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.64, C:0.08, G:0.13, T:0.15
Consensus pattern (18 bp):
AAAATAAAGTAAACATGC
Found at i:29835353 original size:16 final size:16
Alignment explanation
Indices: 29835332--29835377 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
29835322 CATGCGCATG
29835332 AATAAATAATAATAAT
1 AATAAATAATAATAAT
*
29835348 AATAAATAATATTAAT
1 AATAAATAATAATAAT
* *
29835364 GATACAATATTAAT
1 AATA-AATAATAAT
29835378 GTTGCCACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
AATAAATAATAATAAT
Found at i:29835618 original size:23 final size:23
Alignment explanation
Indices: 29835592--29835636 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
29835582 TAGAGATTTG
* *
29835592 AAATCAACAATATACAAATCAAT
1 AAATAAACAATACACAAATCAAT
**
29835615 AAATAAATTATACACAAATCAA
1 AAATAAACAATACACAAATCAA
29835637 CAAAATAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAACAATACACAAATCAAT
Found at i:29835875 original size:19 final size:19
Alignment explanation
Indices: 29835843--29835934 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
29835833 AATCATAACT
29835843 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
29835862 TCTAAAATTACATATCATA
1 TCTAAGATTGCATATCATA
*
29835881 TCTAATATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
29835900 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
29835919 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
29835935 CTTGAAGATT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:29835892 original size:38 final size:38
Alignment explanation
Indices: 29835843--29835934 Score: 166
Period size: 38 Copynumber: 2.4 Consensus size: 38
29835833 AATCATAACT
29835843 TCTAAGATTGCATATCATATCTAAAATTACATATCATA
1 TCTAAGATTGCATATCATATCTAAAATTACATATCATA
* *
29835881 TCTAATATTGCATATCATATCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATATCTAAAATTACATATCATA
29835919 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
29835935 CTTGAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAAATTACATATCATA
Found at i:29836677 original size:44 final size:44
Alignment explanation
Indices: 29836625--29836736 Score: 122
Period size: 44 Copynumber: 2.5 Consensus size: 44
29836615 GCTCTACTTG
*
29836625 CTGTAACTTCAGAGAGATAAGATCT-GTGATTTTAATCCACTCCA
1 CTGTAACTTCAGAGAGATAAGAT-TAGTGACTTTAATCCACTCCA
* * * **
29836669 CTGTAACTTCA-AGGAGATAGGATTATTGGCTTTAATCTGCTCCA
1 CTGTAACTTCAGA-GAGATAAGATTAGTGACTTTAATCCACTCCA
29836713 CTGTAACTTCATG-GAGATAAGATT
1 CTGTAACTTCA-GAGAGATAAGATT
29836737 CGCCATCTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
43 2 0.04
44 55 0.96
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (44 bp):
CTGTAACTTCAGAGAGATAAGATTAGTGACTTTAATCCACTCCA
Found at i:29836852 original size:217 final size:216
Alignment explanation
Indices: 29836577--29836967 Score: 649
Period size: 217 Copynumber: 1.8 Consensus size: 216
29836567 TTTCTTGGGT
* * * *
29836577 CTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATGCGCTCTACTTGCTGTAACTTCAGAGAGA
1 CTGCTCCACTGCAACTTCAGGAAGATAAGACTAGATGCGATCTACTTGCTGCAACTTCAGAGAGA
* *
29836642 TAAGATCTGTGATTTTAATCCACTCCACTGTAACTTCAAGGAGATAGGATTATTGGCTTTAATCT
66 TAAGATCTGTGATTTTAATCCACTCCACTGCAACAT-AAGGAGATAGGATTATTGGCTTTAATCT
* *
29836707 GCTCCACTGTAACTTCATGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTACAACTTTAGGA
130 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTACAACTTTAGGA
29836772 GGATAAGGTTTGCTTACTTAGA
195 GGATAAGGTTTGCTTACTTAGA
*
29836794 CTGCTCCACTGTAACTTCAGGAAGATAAGACTAGATGCGATCTACTCT-CTGCAACTTCAGAGAG
1 CTGCTCCACTGCAACTTCAGGAAGATAAGACTAGATGCGATCTACT-TGCTGCAACTTCAGAGAG
* * *
29836858 ATAAGATCTGTGATTTTAATCCGCTCCACTGCGACATAGGGAGATAGGATTATTGGCTTTAATCT
65 ATAAGATCTGTGATTTTAATCCACTCCACTGCAACATAAGGAGATAGGATTATTGGCTTTAATCT
29836923 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCT
130 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCT
29836968 TTTAAATTGC
Statistics
Matches: 161, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
216 70 0.43
217 90 0.56
218 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (216 bp):
CTGCTCCACTGCAACTTCAGGAAGATAAGACTAGATGCGATCTACTTGCTGCAACTTCAGAGAGA
TAAGATCTGTGATTTTAATCCACTCCACTGCAACATAAGGAGATAGGATTATTGGCTTTAATCTG
CTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTACAACTTTAGGAG
GATAAGGTTTGCTTACTTAGA
Found at i:29837386 original size:44 final size:43
Alignment explanation
Indices: 29837316--29837437 Score: 156
Period size: 44 Copynumber: 2.8 Consensus size: 43
29837306 ATCTGCTATT
* * *
29837316 TTCAACCTACTCCACTGTTGCTCAGGGAGATAGGA-TTCGCAATC
1 TTCAACCTATTCCACTGCTGC-CAGGGAGATAGGACTT-ACAATC
29837360 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTGCTG-CCAGGGAGATAGGACTTACAATC
* *
29837404 TTCAACCTATTCCACTACTGTCCAGTGAGATAGG
1 TTCAACCTATTCCACTGCTG-CCAGGGAGATAGG
29837438 GTTGGGGTCA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
44 67 0.96
45 3 0.04
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (43 bp):
TTCAACCTATTCCACTGCTGCCAGGGAGATAGGACTTACAATC
Found at i:29837499 original size:88 final size:88
Alignment explanation
Indices: 29837448--29838102 Score: 950
Period size: 88 Copynumber: 7.4 Consensus size: 88
29837438 GTTGGGGTCA
* * * * * *
29837448 TCGATATGCTTCGCTGTCAGTGCATGAAGGCAAGATCTGCTATTTTTAACCTGCTTCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTACAAC
29837513 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * *
29837536 TCGATCTGCTTCGTTGTCGGTGCAAGAAGGCAAGATCTGTTATTTTTAACCTGCTCCACTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTACAAC
29837601 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * *
29837624 TCAATCTGCTTCGCTGTCTGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTACAAC
* * *
29837689 CCAAGGAAGCAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * * * *
29837712 TCGATCTGCTTTGCTATCGGTGCAGAAAGGCAAGATTTTCTATTTTTAACCTACTCCACTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTACAAC
29837777 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * * *
29837800 TCGATCTGCTTCGCTGTCAGTGTAGGAAGGCAAGACCTGCAATTTTTAACCTGCTCCACTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTACAAC
*
29837865 CCAGGGAGGCAAGGCCGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
29837888 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTACAAC
* *
29837953 ACAGGGAGGCAAGGCTAGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * *
29837976 TCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTAAAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTACAAC
*
29838041 CCAGGGAGGCAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * *
29838064 TCGATCTTCTTCACTGTCAGTGTAGGAAGGCAAGATCTG
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
29838103 TTATCTTCAC
Statistics
Matches: 508, Mismatches: 59, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 508 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTACAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:29837655 original size:44 final size:44
Alignment explanation
Indices: 29837454--29838009 Score: 154
Period size: 44 Copynumber: 12.6 Consensus size: 44
29837444 GTCATCGATA
* * * * * * *
29837454 TGCTTCGCTGTCAGTGCATGAAGGCAAGATCTGCTATTTTTAACC
1 TGCTTCGCTGTCAGTGCAGGAAGGCAAG-GCTGGTGTCTTCAATC
*** * *
29837499 TGCTTCGCTG-CAACCCAGGGAGGCAAGGCTGGTGTCTTCGATC
1 TGCTTCGCTGTCAGTGCAGGAAGGCAAGGCTGGTGTCTTCAATC
* * * * * * * * *
29837542 TGCTTCGTTGTCGGTGCAAGAAGGCAAGATCTGTTATTTTTAACC
1 TGCTTCGCTGTCAGTGCAGGAAGGCAAG-GCTGGTGTCTTCAATC
* * *** *
29837587 TGCTCCACTG-CAACCCAGGGAGGCAAGGCTGGTGTCTTCAATC
1 TGCTTCGCTGTCAGTGCAGGAAGGCAAGGCTGGTGTCTTCAATC
* * * * * * *
29837630 TGCTTCGCTGTCTGTGCAGGAAGGCAAGATCTGCTATTTTTAACC
1 TGCTTCGCTGTCAGTGCAGGAAGGCAAG-GCTGGTGTCTTCAATC
* * *** * *
29837675 TGCTCCGCT-ACAACCCAAGGAA-GCAAGGTTGGTGTCTTCGATC
1 TGCTTCGCTGTCAGTGC-AGGAAGGCAAGGCTGGTGTCTTCAATC
* * * * ** ** * * * *
29837718 TGCTTTGCTATCGGTGCAGAAAGGCAAGATTTTCTATTTTTAACC
1 TGCTTCGCTGTCAGTGCAGGAAGGCAAG-GCTGGTGTCTTCAATC
* * * * *** * *
29837763 TACTCCACT-ACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATC
1 TGCTTCGCTGTCAGTGCAGGAAGGCAAGGCTGGTGTCTTCAATC
* * *** * * *
29837806 TGCTTCGCTGTCAGTGTAGGAAGGCAAGACCTGCAATTTTTAACC
1 TGCTTCGCTGTCAGTGCAGGAAGGCAAG-GCTGGTGTCTTCAATC
* * *** * * *
29837851 TGCTCCACTG-CAACCCAGGGAGGCAAGGCCGGTGTCTTCGATC
1 TGCTTCGCTGTCAGTGCAGGAAGGCAAGGCTGGTGTCTTCAATC
* * * * * * *
29837894 TGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACC
1 TGCTTCGCTGTCAGTGCAGGAAGGCAAG-GCTGGTGTCTTCAATC
* *** * * *
29837939 TGCTCCGCTG-CAACACAGGGAGGCAAGGCTAGTGTCTTCGATC
1 TGCTTCGCTGTCAGTGCAGGAAGGCAAGGCTGGTGTCTTCAATC
* *
29837982 TACTTCGCTGTCGGTGCAGGAAGGCAAG
1 TGCTTCGCTGTCAGTGCAGGAAGGCAAG
29838010 ATCTGCTATT
Statistics
Matches: 325, Mismatches: 173, Indels: 27
0.62 0.33 0.05
Matches are distributed among these distances:
43 99 0.30
44 131 0.40
45 95 0.29
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (44 bp):
TGCTTCGCTGTCAGTGCAGGAAGGCAAGGCTGGTGTCTTCAATC
Found at i:29837948 original size:45 final size:45
Alignment explanation
Indices: 29837893--29838035 Score: 130
Period size: 44 Copynumber: 3.2 Consensus size: 45
29837883 TGTCTTCGAT
*
29837893 CTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAC
1 CTGCTCCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAC
**** * * * * ** *
29837938 CTGCTCCGCTG-CAACACAGGGAGGCAAG-GCTAG-TGTCTTCGAT
1 CTGCTCCGCTGTCGGTGCAGGAAGGCAAGATCT-GCTATTTTTAAC
* *
29837981 CTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAC
1 CTGCTCCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAC
29838026 CTGCTCCGCT
1 CTGCTCCGCT
29838036 AAAACCCAGG
Statistics
Matches: 67, Mismatches: 27, Indels: 8
0.66 0.26 0.08
Matches are distributed among these distances:
43 16 0.24
44 26 0.39
45 25 0.37
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.28
Consensus pattern (45 bp):
CTGCTCCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAC
Found at i:29839330 original size:2 final size:2
Alignment explanation
Indices: 29839323--29839357 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29839313 TTTCTTCTTT
29839323 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
29839358 TTTTAATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:29840364 original size:26 final size:25
Alignment explanation
Indices: 29840304--29840373 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
29840294 AAGAAAATCC
* *
29840304 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAAT-ATTAGTTCA
* *
29840330 AAAAAAATGAAAAAATATTGGTTCA
1 AAAAGAATGAAAAAATATTAGTTCA
* *
29840355 AAAATGAATGCAAAGATAT
1 AAAA-GAATGAAAAAATAT
29840374 ATTTTATTAG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 11 0.31
26 25 0.69
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (25 bp):
AAAAGAATGAAAAAATATTAGTTCA
Found at i:29845157 original size:19 final size:19
Alignment explanation
Indices: 29845133--29845243 Score: 195
Period size: 19 Copynumber: 5.8 Consensus size: 19
29845123 AATCATATCT
29845133 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
29845152 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
29845171 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
29845190 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
29845209 TCTAAGATTACATATCATG
1 TCTAAGATTGCATATCATA
29845228 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
29845244 CTTGAAGATT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 87 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:29845182 original size:38 final size:38
Alignment explanation
Indices: 29845110--29845243 Score: 187
Period size: 38 Copynumber: 3.4 Consensus size: 38
29845100 AAATTAAATC
*
29845110 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
29845152 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* * *
29845190 TCTAAGATTGCATATCATATCTAAGATTACATATCATG
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
*
29845228 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
29845244 CTTGAAGATT
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
38 70 0.80
41 7 0.08
42 11 0.12
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:29849086 original size:11 final size:11
Alignment explanation
Indices: 29849070--29849104 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
29849060 TCTGGACTCC
29849070 ACCATTGTTGA
1 ACCATTGTTGA
*
29849081 ACCATTGTCGA
1 ACCATTGTTGA
*
29849092 ACCACTGTTGA
1 ACCATTGTTGA
29849103 AC
1 AC
29849105 ATTTTTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (11 bp):
ACCATTGTTGA
Found at i:29857005 original size:25 final size:25
Alignment explanation
Indices: 29856976--29857028 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
29856966 GACTTAGTGT
29856976 ATTTATCCATGATATAGGTAGATTC
1 ATTTATCCATGATATAGGTAGATTC
*
29857001 ATTTATCCATGATATAGGTATATTC
1 ATTTATCCATGATATAGGTAGATTC
29857026 ATT
1 ATT
29857029 CATAGCATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.43
Consensus pattern (25 bp):
ATTTATCCATGATATAGGTAGATTC
Found at i:29866618 original size:23 final size:24
Alignment explanation
Indices: 29866569--29866629 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
29866559 TTAAAAATTC
29866569 AAAAATTTTAAAATATATATTTAA
1 AAAAATTTTAAAATATATATTTAA
*
29866593 AAAAATTTTAAAATATAT-TTTTA
1 AAAAATTTTAAAATATATATTTAA
*
29866616 AAAGATTTTAAAAT
1 AAAAATTTTAAAAT
29866630 TAAAAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 17 0.49
24 18 0.51
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAAAATTTTAAAATATATATTTAA
Found at i:29868731 original size:27 final size:27
Alignment explanation
Indices: 29868693--29868759 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
29868683 CAAGAGACTG
*
29868693 ATAGGCGGCACCAAAGGTGTCATTCCC
1 ATAGGCGGCACCAAAGGTGCCATTCCC
* *
29868720 ATAGGCGGCACCGATGGTGCCATTCCC
1 ATAGGCGGCACCAAAGGTGCCATTCCC
*
29868747 ATGGGCGGCACCA
1 ATAGGCGGCACCA
29868760 CTCGTGTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.30, T:0.16
Consensus pattern (27 bp):
ATAGGCGGCACCAAAGGTGCCATTCCC
Found at i:29869089 original size:40 final size:36
Alignment explanation
Indices: 29869029--29869114 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 36
29869019 AAACTAGTAT
* * *
29869029 TATTATTATGGTTAGTTATTATTTTTAGTA-AAACCC
1 TATTATTATTGTTAGTTATTATTTTGAGTATAAA-AC
29869065 TAATTATTATTGTTAGTTACTATTATTTTGAGTATAAAAC
1 T-ATTATTATTGTTAG-T--TATTATTTTGAGTATAAAAC
29869105 TATTATTATT
1 TATTATTATT
29869115 TTTATTGAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 1 0.02
37 13 0.31
38 1 0.02
39 9 0.21
40 15 0.36
41 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (36 bp):
TATTATTATTGTTAGTTATTATTTTGAGTATAAAAC
Found at i:29871776 original size:159 final size:154
Alignment explanation
Indices: 29871416--29871836 Score: 437
Period size: 159 Copynumber: 2.7 Consensus size: 154
29871406 GCATGTTGAA
* *
29871416 AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCGTTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTA
*
29871481 -TTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTAAGTGCATTATGTTTGA
66 CTTTTAAAAAAATAT-ATAATTTCTAATTTTATAATTTTACATTATTTAAGTACATTATGTTTGA
* *
29871545 AATTTATTATTTTAGTGTATTTTTT
130 AATTTATTATTTTACTGTAATTTTT
* * * * * * * *
29871570 AAATTAATTTAGTGTCAAAAAAACCCTTA-TTCCTGCCCTTTGC-TCGTATTATTTTC-CTGAAT
1 AAA-AAATTTA--GT--AAAACACTCTTACTT-CGGCCATTT-CTTCGTATTTTTTTCTCCGCAT
* * * *
29871632 TTTATTACTTTTAATAAAAA-ATATTATTTTCGT-ATTTTATTATTTTATATTATTTCAGTACAT
59 TTTATTACTTTTAA-AAAAATATA-TAATTTC-TAATTTTATAATTTTACATTATTTAAGTACAT
* *
29871695 TTTGTTTGAAATATTTGTATTAATTATTTCTG-AATTTTT
121 TATGTTTG-AA-A-TT-TATT-ATT-TTACTGTAATTTTT
29871734 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTA
*
29871799 C-TTT-AAAAAATATCATAATTTCTAATTTTATAAATTTA
66 CTTTTAAAAAAATAT-ATAATTTCTAATTTTATAATTTTA
29871837 TGAATTTAGT
Statistics
Matches: 214, Mismatches: 30, Indels: 42
0.75 0.10 0.15
Matches are distributed among these distances:
154 3 0.01
155 5 0.02
157 8 0.04
158 35 0.16
159 109 0.51
160 23 0.11
161 3 0.01
162 2 0.01
163 10 0.05
164 12 0.06
165 4 0.02
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (154 bp):
AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTA
CTTTTAAAAAAATATATAATTTCTAATTTTATAATTTTACATTATTTAAGTACATTATGTTTGAA
ATTTATTATTTTACTGTAATTTTT
Found at i:29872056 original size:286 final size:286
Alignment explanation
Indices: 29871544--29872412 Score: 1513
Period size: 286 Copynumber: 3.0 Consensus size: 286
29871534 ATTATGTTTG
* * *
29871544 AAATTTATTATTTTAGTGTATTTTTTAAATTAATTTAGTGTCAAAAAAACCCTTATTCCTGCCCT
1 AAATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCT
** *
29871609 TTGCTCGTATTATTTTCCTGAATTTTATTACTTTTAATAAAAAATATTATTTTCGTATTTTATTA
66 TTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTA
*
29871674 TTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAA
131 TTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTTAAAAA
29871739 ATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTACTTTA
196 ATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTACTTTA
29871804 AAAAATATCATAATTTCTAATTTTAT
261 AAAAATATCATAATTTCTAATTTTAT
* *
29871830 AAATTTATGAATTTAGTGTGTTTTTAAAATTAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCT
1 AAATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCT
*
29871895 TTGCTCGTATTATTTTCCCAAATTTTGTTACTTTCAATAAAAAATATTATTTTCGTATTTTATTA
66 TTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTA
29871960 TTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTTAAAAA
131 TTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTTAAAAA
**
29872025 ATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTTCTCCATATTTTATTACTTT
196 ATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTA-TTTTTTTCTCCGCATTTTATTACTTT
29872090 AAAAAATATCATAATTTCTAATTTTAT
260 AAAAAATATCATAATTTCTAATTTTAT
* *
29872117 AAATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAAACCATTATTCCTACCC
1 AAATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGT-AAAAAAAACCCTTATTCCTGCCC
29872182 TTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATT
65 TTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATT
* * *
29872247 ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTTTTAATTCTTAAAA
130 ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTTAAAA
* ** *
29872312 AATTTAGTAAAACACTCTTACTCCGGCCATTTCTTCGTATTTTTTTCTTTGCATCTTATTACTTT
195 AATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTACTTT
*
29872377 AAAAAATATCATAATTTTTAATTTTAT
260 AAAAAATATCATAATTTCTAATTTTAT
*
29872404 AATTTTATT
1 AAATTTATT
29872413 TTATTTTAGT
Statistics
Matches: 553, Mismatches: 28, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
286 223 0.40
287 145 0.26
288 185 0.33
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (286 bp):
AAATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCT
TTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTA
TTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTTAAAAA
ATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTACTTTA
AAAAATATCATAATTTCTAATTTTAT
Found at i:29872850 original size:4 final size:4
Alignment explanation
Indices: 29872841--29872894 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
29872831 CTCCTTTCAT
*
29872841 TTTC TTTC TTTC TTTCC TCTCC TTTC -TT- TTTC TTTC TTTC TTTC -TTC
1 TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
29872888 -TTC TTTC
1 TTTC TTTC
29872895 CCTCTCTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
3 10 0.23
4 28 0.65
5 4 0.09
6 1 0.02
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:29872871 original size:28 final size:28
Alignment explanation
Indices: 29872807--29872894 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
29872797 TCCACTCTTC
* *
29872807 TTCTTCTTC-TTCTTTTTTTCTCTTCTCCT
1 TTCTTTTTCTTTCTTTCTTTC-C-TCTCCT
*
29872836 TTCATTTTCTTTCTTTCTTTCCTCTCCT
1 TTCTTTTTCTTTCTTTCTTTCCTCTCCT
* *
29872864 TTCTTTTTCTTTCTTTCTTTCTTCTTCT
1 TTCTTTTTCTTTCTTTCTTTCCTCTCCT
29872892 TTC
1 TTC
29872895 CCTCTCTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
28 34 0.65
29 8 0.15
30 10 0.19
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (28 bp):
TTCTTTTTCTTTCTTTCTTTCCTCTCCT
Found at i:29872891 original size:18 final size:18
Alignment explanation
Indices: 29872810--29872894 Score: 70
Period size: 18 Copynumber: 4.7 Consensus size: 18
29872800 ACTCTTCTTC
29872810 TTCTTCTTCTTT-TTT-T
1 TTCTTCTTCTTTCTTTCT
* *
29872826 CTCTTCTCCTTTCATTTTCT
1 TTCTTCTTCTTTC--TTTCT
*
29872846 TTC-T-TTCTTTCCTCTCCT
1 TTCTTCTTCTTT-CT-TTCT
*
29872864 TTCTTTTTCTTTCTTTCT
1 TTCTTCTTCTTTCTTTCT
29872882 TTCTTCTTCTTTC
1 TTCTTCTTCTTTC
29872895 CCTCTCTTTC
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
16 10 0.19
17 1 0.02
18 26 0.48
19 8 0.15
20 9 0.17
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.69
Consensus pattern (18 bp):
TTCTTCTTCTTTCTTTCT
Found at i:29872902 original size:28 final size:28
Alignment explanation
Indices: 29872816--29872905 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
29872806 CTTCTTCTTC
* ** *
29872816 TTCTTTTTTTCTCTTCTCCTTTCATTTTCT
1 TTCTTTCTTTC-C-TCTCCTTTCCCTCTCT
** *
29872846 TTCTTTCTTTCCTCTCCTTTCTTTTTCT
1 TTCTTTCTTTCCTCTCCTTTCCCTCTCT
* *
29872874 TTCTTTCTTTCTTCTTCTTTCCCTCTCT
1 TTCTTTCTTTCCTCTCCTTTCCCTCTCT
29872902 TTCT
1 TTCT
29872906 CTTCCCCCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
28 42 0.79
29 1 0.02
30 10 0.19
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (28 bp):
TTCTTTCTTTCCTCTCCTTTCCCTCTCT
Found at i:29872905 original size:14 final size:13
Alignment explanation
Indices: 29872847--29872910 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 13
29872837 TCATTTTCTT
29872847 TCTTTCTTTCCTC
1 TCTTTCTTTCCTC
* *
29872860 TCCTTTCTTTTTCTT
1 T-CTTTC-TTTCCTC
29872875 TCTTTCTTT-CT-
1 TCTTTCTTTCCTC
29872886 TC-TTCTTTCCCTC
1 TCTTTCTTT-CCTC
29872899 TCTTTCTCTTCC
1 TCTTTCT-TTCC
29872911 CCCCACCTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
10 6 0.14
11 2 0.05
12 4 0.10
13 6 0.14
14 16 0.38
15 8 0.19
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
TCTTTCTTTCCTC
Found at i:29875446 original size:39 final size:38
Alignment explanation
Indices: 29875403--29875500 Score: 97
Period size: 39 Copynumber: 2.5 Consensus size: 38
29875393 AATTCGCAAC
* * * *
29875403 AAATGTTGAATCTCGTTATATTGCCGGAGGATCCACATA
1 AAATGTT-AATCTCGTTATATTACCGAAGGATCCAAAAA
* * *
29875442 AAATGCTAGATCTCGTTATATTACCTAAGGATCTAAAAA
1 AAATGTTA-ATCTCGTTATATTACCGAAGGATCCAAAAA
*
29875481 AAATGTTAAATCTCATTATA
1 AAATGTT-AATCTCGTTATA
29875501 ATTTTGACAA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
38 1 0.02
39 46 0.96
40 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (38 bp):
AAATGTTAATCTCGTTATATTACCGAAGGATCCAAAAA
Found at i:29875826 original size:15 final size:15
Alignment explanation
Indices: 29875806--29875834 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29875796 GTCAAAATTC
29875806 ACAACAATTTTCACT
1 ACAACAATTTTCACT
29875821 ACAACAATTTTCAC
1 ACAACAATTTTCAC
29875835 ATAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (15 bp):
ACAACAATTTTCACT
Found at i:29889639 original size:44 final size:45
Alignment explanation
Indices: 29889575--29889706 Score: 128
Period size: 44 Copynumber: 3.0 Consensus size: 45
29889565 AGTCATCGTG
*
29889575 GCAAATCCT-ATCTCTCTGAAGTTGCAGTGAAGCAGATTAAAGCCA
1 GCAAAT-CTGATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCA
* * * **
29889620 -CAAAT-TAGATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGATA
1 GCAAATCT-GATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCA
* * *
29889664 GCAAATCTTATCTCCCTGAAGTTACAGT-AGAGTAGATTAAAGC
1 GCAAATCTGATCTCCCTGAAGTTGCAGTGA-AGCAGATTAAAGC
29889707 TATAAACCTT
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
42 1 0.01
44 35 0.51
45 32 0.46
46 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (45 bp):
GCAAATCTGATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCA
Found at i:29889701 original size:89 final size:88
Alignment explanation
Indices: 29889575--29890699 Score: 495
Period size: 89 Copynumber: 12.4 Consensus size: 88
29889565 AGTCATCGTG
* * *
29889575 GCAAATCCTATCTCTCTGAAGTTGCAGT-GAAGCAGATTAAAGCCACAAATTAGATCTCCCTGAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTAG-AGCAGATTAAAGCTACAAATTA-ATCTCCCTGAA
* *
29889639 GTTGTAGTGGAGCAGACTAAAGATA
64 GTTGCAGTGGAGCAGACTGAAGATA
* * * *
29889664 GCAAATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTAAAGCTATAAACCTT-ATCTCCCTAAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACAAA--TTAATCTCCCTGAA
* * ** *
29889728 GTTACAGTGGGGCAGGTTGAAGTTA
64 GTTGCAGTGGAGCAGACTGAAGATA
* * * * * * * * * *
29889753 -CAAGTCTTATCTCTC-AAAATTGCAGTGGGGCAGATTGAAGTTACAAGTCTAATCCCCCTGAAG
1 GCAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACAAAT-TAATCTCCCTGAAG
**
29889816 TTGCAGCAGAGCAGACTGAAGATA
65 TTGCAGTGGAGCAGACTGAAGATA
* * ** *
29889840 GCGAATCTTATTTCCCTGAAGTTGCAGTAGAATAGATTAAGGCTACAAATTACAAATCGGATCCC
1 GCAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACAAATT---AATC---T-CC
* * * *
29889905 CTTGAAGTTGTAGTGGGGCAGATTGAAGTTA
59 C-TGAAGTTGCAGTGGAGCAGACTGAAGATA
* * ** * * * * ** * *
29889936 -CGAGTCTTATCTCCCTGAAGTTGTTGTGGAACAGACTAAAGATAGCAAATCTTGTTTCCCTAAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTA-CAAAT-TAATCTCCCTGAA
* * * *
29890000 GTTGCAGTGGAACA-AATTAAGGCTA
64 GTTGCAGTGGAGCAGACTGAA-GATA
* * * * * * * *
29890025 -CAAATTACAATCGGATCTCCCTGAAGTTGTAGTGGGGCAGATTGAAGATACAAGTCTTATCTCC
1 GCAAA-T-C--T--TATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACAAAT-TAATCTCC
*
29890089 CTGAAGTTGCAGTGGAGCAAACTGAAGATA
59 CTGAAGTTGCAGTGGAGCAGACTGAAGATA
** * ** * *
29890119 GCAAATCTTATCTTTCTAAAGTTATAGTAGAGCAAATTAAAGCTATAAACCTT-ATCTCCCTGAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACAAA--TTAATCTCCCTGAA
** * ** *
29890183 GTTATAGTGGGGCAGGTTGAAGTTA
64 GTTGCAGTGGAGCAGACTGAAGATA
* * * * * * * * * * * *
29890208 -CAAGTCTTATCT-CCTAAAATTTACAGTGGGGCAGATTGAAGTTACAAGTCTTATCCCCCTAAA
1 GCAAATCTTATCTCCCT-GAAGTTGCAGTAGAGCAGATTAAAGCTACAAAT-TAATCTCCCTGAA
29890271 GTTGCAGTGGAGCAGACTGAAGATA
64 GTTGCAGTGGAGCAGACTGAAGATA
* * * * ** *
29890296 G-AGAACCTTATTTCCATGAAGTTGCAGTGGAATAGATTAAGGCTACAAATTACAAATCGGATCC
1 GCA-AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACAAATT---AATC---T-C
* * * * *
29890360 CCTTG-AGTTGCAGTGGGGTAGATTAAAGTTA
58 CC-TGAAGTTGCAGTGGAGCAGACTGAAGATA
* * * * * * * * *
29890391 -CGAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAGATAGCAAATCTTATTTCCCTAAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTA-CAAAT-TAATCTCCCTGAA
* * * *
29890455 GTTGCAGTGGAACA-AATTAAGGCTA
64 GTTGCAGTGGAGCAGACTGAA-GATA
* * * * * * ** * * *
29890480 -CAAATTACAATCGGATCTCCTTGAAGTTGTAGTGGGGTAGATCGAAGATACAAGTTTTATCTCC
1 GCAAA-T-C--T--TATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACAA-ATTAATCTCC
* *
29890544 CTGAAGTTGCAGTGGAGTAGACTAAAGATA
59 CTGAAGTTGCAGTGGAGCAGACTGAAGATA
* * * *
29890574 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAATTAAAGCTATAAACCTT-ATCTCCTTGAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACAAA--TTAATCTCCCTGAA
* *
29890638 GATGCAGTGGAGCAGGA-TGAAG-TT
64 GTTGCAGTGGAGCA-GACTGAAGATA
* * *
29890662 GCTAATCTTATCTCCATGAAGATGCAGTAGAGCAGATT
1 GCAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT
29890700 GAATATACTA
Statistics
Matches: 766, Mismatches: 211, Indels: 119
0.70 0.19 0.11
Matches are distributed among these distances:
85 1 0.00
86 2 0.00
87 52 0.07
88 132 0.17
89 273 0.36
90 14 0.02
91 15 0.02
93 6 0.01
94 97 0.13
95 143 0.19
96 30 0.04
97 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (88 bp):
GCAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACAAATTAATCTCCCTGAAGT
TGCAGTGGAGCAGACTGAAGATA
Found at i:29890104 original size:139 final size:139
Alignment explanation
Indices: 29889776--29890278 Score: 576
Period size: 139 Copynumber: 3.7 Consensus size: 139
29889766 TCAAAATTGC
* * **
29889776 AGTGGGGCAGATTGAAGTTACAAGTCTAATCCCCCTGAAGTTGCAGCAGAGCAGACTGAAGATAG
1 AGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
* * * *
29889841 CGAATCTTATTTCCCTGAAGTTGCAGTAGAATAGATTAAGGCTACAAATTACAAATCGGATC-CC
66 CAAATCTTATTTCCCTAAAGTTGCAGTAGAACAAATTAAGGCTACAAATTAC-AATCGGATCTCC
29889905 CTTGAAGTTGT
130 C-TGAAGTTGT
* ** * *
29889916 AGTGGGGCAGATTGAAGTTACGAGTCTTATCTCCCTGAAGTTGTTGTGGAACAGACTAAAGATAG
1 AGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
* *
29889981 CAAATCTTGTTTCCCTAAAGTTGCAGTGGAACAAATTAAGGCTACAAATTACAATCGGATCTCCC
66 CAAATCTTATTTCCCTAAAGTTGCAGTAGAACAAATTAAGGCTACAAATTACAATCGGATCTCCC
29890046 TGAAGTTGT
131 TGAAGTTGT
* *
29890055 AGTGGGGCAGATTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAG
1 AGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
* ** * * * **
29890120 CAAATCTTATCTT-TCTAAAGTTATAGTAGAGCAAATTAAAGCT----A-TA-AACCTTATCTCC
66 CAAATCTTAT-TTCCCTAAAGTTGCAGTAGAACAAATTAAGGCTACAAATTACAATCGGATCTCC
*
29890178 CTGAAGTTAT
130 CTGAAGTTGT
* * * * * * *
29890188 AGTGGGGCAGGTTGAAGTTACAAGTCTTATCT-CCTAAAATTTACAGTGGGGCAGATTGAAGTTA
1 AGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCT-GAAGTTGCAGTGGAGCAGACTGAAGATA
* **
29890252 -CAAGTCTTATCCCCCTAAAGTTGCAGT
65 GCAAATCTTATTTCCCTAAAGTTGCAGT
29890279 GGAGCAGACT
Statistics
Matches: 311, Mismatches: 48, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
132 23 0.07
133 69 0.22
134 2 0.01
135 1 0.00
139 109 0.35
140 107 0.34
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (139 bp):
AGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
CAAATCTTATTTCCCTAAAGTTGCAGTAGAACAAATTAAGGCTACAAATTACAATCGGATCTCCC
TGAAGTTGT
Found at i:29890124 original size:95 final size:95
Alignment explanation
Indices: 29889944--29890124 Score: 222
Period size: 95 Copynumber: 1.9 Consensus size: 95
29889934 TACGAGTCTT
* * *
29889944 ATCTCCCTGAAGTTGTTGTGGAACAGACTAAAGATAGCAAATCTTGTTTCCCTAAAGTTGCAGTG
1 ATCTCCCTGAAGTTGTAGTGGAACAGACTAAAGATAGCAAATCTTATCTCCCTAAAGTTGCAGTG
* *
29890009 GAACAAATTAAGGCTACAAATTACAATCGG
66 GAACAAATGAAGGATACAAATTACAATCGG
** * * * *
29890039 ATCTCCCTGAAGTTGTAGTGGGGCAGATTGAAGATA-CAAGTCTTATCTCCCTGAAGTTGCAGTG
1 ATCTCCCTGAAGTTGTAGTGGAACAGACTAAAGATAGCAAATCTTATCTCCCTAAAGTTGCAGTG
*
29890103 GAGCAAACTGAA-GATAGCAAAT
66 GAACAAA-TGAAGGATA-CAAAT
29890125 CTTATCTTTC
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
94 33 0.46
95 39 0.54
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (95 bp):
ATCTCCCTGAAGTTGTAGTGGAACAGACTAAAGATAGCAAATCTTATCTCCCTAAAGTTGCAGTG
GAACAAATGAAGGATACAAATTACAATCGG
Found at i:29890325 original size:133 final size:133
Alignment explanation
Indices: 29889628--29890325 Score: 339
Period size: 139 Copynumber: 5.2 Consensus size: 133
29889618 CACAAATTAG
* * * * * * *
29889628 ATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGATAGCAAATCTTATCTCCCTGAAGTTACAGTA
1 ATCTCCATGAAGTTGTAGTGGGGCAGATTGAAGATA-CAAGTCTTATCTCCCTAAAGTTACAGTG
* * * * * * * * * * *** * * * *
29889693 GAGTAGATTAAAGCTA-TAAACCTTATCTCCCTAAAGTTACAGTGGGGCAGGTTGAAGTTACAAG
65 GAGCAAACTGAAGATAGCAAATCTTATCCCCCTAAAGTTACAGTAGAGCAAACTAAAGATAGAAA
*
29889757 TCTT
130 CCTT
* * * * * * * **
29889761 ATCTCTCA--AAATTGCAGTGGGGCAGATTGAAGTTACAAGTCTAATCCCCCTGAAGTTGCAGCA
1 ATCTC-CATGAAGTTGTAGTGGGGCAGATTGAAGATACAAGTCTTATCTCCCTAAAGTTACAGTG
* * ** * *
29889824 GAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTAGAATAG-ATTAAGGCTACAA
65 GAGCAAACTGAAGATAGCAAATCTTATCCCCCTAAAGTTACAGTAG---AGCA--AA--CTA-AA
* * **
29889888 -ATTACAAATCGG
122 GA-TAGAAACCTT
* * * * * ***
29889900 ATCCCCTTGAAGTTGTAGTGGGGCAGATTGAAGTTACGAGTCTTATCTCCCTGAAGTTGTTGTGG
1 ATCTCCATGAAGTTGTAGTGGGGCAGATTGAAGATACAAGTCTTATCTCCCTAAAGTTACAGTGG
* * * * ** * * * * * * *
29889965 AACAGACTAAAGATAGCAAATCTTGTTTCCCTAAAGTTGCAGTGGAACAAATTAAGGCTACAAAT
66 AGCAAACTGAAGATAGCAAATCTTATCCCCCTAAAGTTACAGTAGAGCAAACTAAAGATA-GAA-
**
29890030 TACAATCGG
129 -AC---CTT
* * *
29890039 ATCTCCCTGAAGTTGTAGTGGGGCAGATTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAGTGG
1 ATCTCCATGAAGTTGTAGTGGGGCAGATTGAAGATACAAGTCTTATCTCCCTAAAGTTACAGTGG
*** * * * *
29890104 AGCAAACTGAAGATAGCAAATCTTATCTTTCTAAAGTTATAGTAGAGCAAATTAAAGCTATAAAC
66 AGCAAACTGAAGATAGCAAATCTTATCCCCCTAAAGTTACAGTAGAGCAAACTAAAGATAGAAAC
29890169 CTT
131 CTT
* * * * *
29890172 ATCTCCCTGAAGTTATAGTGGGGCAGGTTGAAGTTACAAGTCTTATCT-CCTAAAATTTACAGTG
1 ATCTCCATGAAGTTGTAGTGGGGCAGATTGAAGATACAAGTCTTATCTCCCT-AAAGTTACAGTG
* * * * * * * * *
29890236 GGGCAGATTGAAGTTA-CAAGTCTTATCCCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGAGA
65 GAGCAAACTGAAGATAGCAAATCTTATCCCCCTAAAGTTACAGTAGAGCAAACTAAAGATAGA-A
29890300 ACCTT
129 ACCTT
* *
29890305 ATTTCCATGAAGTTGCAGTGG
1 ATCTCCATGAAGTTGTAGTGG
29890326 AATAGATTAA
Statistics
Matches: 440, Mismatches: 102, Indels: 46
0.75 0.17 0.08
Matches are distributed among these distances:
131 35 0.08
132 80 0.18
133 98 0.22
134 6 0.01
135 1 0.00
136 5 0.01
137 1 0.00
138 5 0.01
139 123 0.28
140 86 0.20
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (133 bp):
ATCTCCATGAAGTTGTAGTGGGGCAGATTGAAGATACAAGTCTTATCTCCCTAAAGTTACAGTGG
AGCAAACTGAAGATAGCAAATCTTATCCCCCTAAAGTTACAGTAGAGCAAACTAAAGATAGAAAC
CTT
Found at i:29890397 original size:139 final size:138
Alignment explanation
Indices: 29890231--29890618 Score: 528
Period size: 139 Copynumber: 2.8 Consensus size: 138
29890221 CTAAAATTTA
* * * *
29890231 CAGTGGGGCAGATTGAAGTTACAAGTCTTATCCCCCTAAAGTTGCAGTGGAGCAGACTGAAGATA
1 CAGTGGGGTAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATA
* * *
29890296 G-AGAACCTTATTTCCATGAAGTTGCAGTGGAATAGATTAAGGCTACAAATTACAAATCGGATCC
66 GCA-AATCTTATTTCC-TGAAGTTGCAGTGGAACAAATTAAGGCTACAAATTAC-AATCGGATCC
29890360 CCTTG-AGTTG
128 CCTTGAAGTTG
* * *
29890370 CAGTGGGGTAGATTAAAGTTACGAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAGATA
1 CAGTGGGGTAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATA
* *
29890435 GCAAATCTTATTTCCCTAAAGTTGCAGTGGAACAAATTAAGGCTACAAATTACAATCGGATCTCC
66 GCAAATCTTATTT-CCTGAAGTTGCAGTGGAACAAATTAAGGCTACAAATTACAATCGGATCCCC
29890500 TTGAAGTTG
130 TTGAAGTTG
* * * * *
29890509 TAGTGGGGTAGATCGAAGATACAAGTTTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAAGATA
1 CAGTGGGGTAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATA
* * * *
29890574 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAATTAAAGCTA
66 GCAAATCTTATTTC-CTGAAGTTGCAGTGGAACAAATTAAGGCTA
29890619 TAAACCTTAT
Statistics
Matches: 220, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
138 15 0.07
139 202 0.92
140 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (138 bp):
CAGTGGGGTAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATA
GCAAATCTTATTTCCTGAAGTTGCAGTGGAACAAATTAAGGCTACAAATTACAATCGGATCCCCT
TGAAGTTG
Done.