Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold14
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: 2879421
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 64274 characters in sequence are not A, C, G, or T
File 14 of 17
Found at i:2254632 original size:21 final size:20
Alignment explanation
Indices: 2254606--2254682 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
2254596 CTGCCAAGAA
*
2254606 ATGTATCGATACATATTTTTT
1 ATGTATCGATACAT-TTTTTC
****
2254627 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTTTTTC
2254647 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TTTTTC
2254668 ATGTATCGATACATT
1 ATGTATCGATACATT
2254683 GCAACATGTA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTC
Found at i:2254652 original size:20 final size:20
Alignment explanation
Indices: 2254627--2254699 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2254617 CATATTTTTT
2254627 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2254647 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2254668 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2254688 ATGTATCGATAC
1 ATGTATCGATAC
2254700 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2254666 original size:41 final size:41
Alignment explanation
Indices: 2254606--2254699 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2254596 CTGCCAAGAA
*
2254606 ATGTATCGATACATATTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
*
2254647 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
2254688 ATGTATCGATAC
1 ATGTATCGATAC
2254700 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
Found at i:2255232 original size:132 final size:133
Alignment explanation
Indices: 2254994--2255369 Score: 429
Period size: 132 Copynumber: 2.8 Consensus size: 133
2254984 CCTAACAGTA
* ** * * *
2254994 GGTTTGTATGGTTTTATCTCAACCAACCCCTTTTT-GACTTAGGTTTCGCCTTAGTCACCCTTAG
1 GGTTTGTATGGTTTCATCTCGGCCAACCCCTTTTTCAACTTAGGTTTCGCCTTGGTCACCCTAAG
* * * * *
2255058 TTGGGTTGCATAGTTTCATC-CTAGCCAACTCTCTTTT-GACTTAGGTTCCACCTTGGTCACCTT
66 TTGGTTTGTATGGTTTCATCTC-AGCCAACCCT-TTTTCGACTTAGGTTCCACCTTGGTCACCGT
*
2255121 TAGTT
129 AAGTT
* *
2255126 GGTTTGTATGGTTTCATCCCGGCCAA-CCCTTTTTCAACTTAGGTTTTGCCTTGGTCACCCTAAG
1 GGTTTGTATGGTTTCATCTCGGCCAACCCCTTTTTCAACTTAGGTTTCGCCTTGGTCACCCTAAG
* ***
2255190 TTGGTTTGTATGGTTTCATCTCAGCCAACCCTTTTTCAACTTAGGTTTTGCCTTGGTCACCGTAA
66 TTGGTTTGTATGGTTTCATCTCAGCCAACCCTTTTTCGACTTAGGTTCCACCTTGGTCACCGTAA
2255255 GTT
131 GTT
* * * ** * *
2255258 GGTTCGTAGGGTTTCATCTCGGCTAATTCC-TTTTCTACTTAGGTTTGGCCTTGGTCACCCTAAG
1 GGTTTGTATGGTTTCATCTCGGCCAACCCCTTTTTCAACTTAGGTTTCGCCTTGGTCACCCTAAG
* ** * *
2255322 TTTGTTCATATGGTTTCATCTCGGCCAACCTTTTTTCGACTTAGGTTC
66 TTGGTTTGTATGGTTTCATCTCAGCCAACCCTTTTTCGACTTAGGTTC
2255370 TACCCTAGTC
Statistics
Matches: 208, Mismatches: 32, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
131 12 0.06
132 193 0.93
133 3 0.01
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (133 bp):
GGTTTGTATGGTTTCATCTCGGCCAACCCCTTTTTCAACTTAGGTTTCGCCTTGGTCACCCTAAG
TTGGTTTGTATGGTTTCATCTCAGCCAACCCTTTTTCGACTTAGGTTCCACCTTGGTCACCGTAA
GTT
Found at i:2255336 original size:198 final size:198
Alignment explanation
Indices: 2254994--2255368 Score: 463
Period size: 198 Copynumber: 1.9 Consensus size: 198
2254984 CCTAACAGTA
* * *
2254994 GGTTTGTATGGTTTTATCTCAACCAACCCCTTTTTGACTTAGGTTTCGCCTTAGTCACCCTTAGT
1 GGTTTGTATGGTTTCATCTCAACCAACCCCTTTTTAACTTAGGTTTCGCCTTAGTCACCCTAAGT
* *
2255059 TGGGTTGCATAGTTTCATCCTAGCCAACTCTCTTTTGACTTAGGTTCCACCTTGGTCACCTTTAG
66 TGGGTTGCATAGTTTCATCCTAGCCAACTCTCTTTTGACTTAGGTTCCACCTTGGTCACCCTAAG
**
2255124 TTGGTTTGTATGGTTTCATCCCGGCCAACCCTTTTTCAACTTAGGTTTTGCCTTGGTCACCCTAA
131 TTGGTTCATATGGTTTCATCCCGGCCAACCCTTTTTCAACTTAGGTTTTGCCTTGGTCACCCTAA
2255189 GTT
196 GTT
* * * *
2255192 GGTTTGTATGGTTTCATCTCAGCCAA-CCCTTTTTCAACTTAGGTTTTGCCTTGGTCACCGTAAG
1 GGTTTGTATGGTTTCATCTCAACCAACCCCTTTTT-AACTTAGGTTTCGCCTTAGTCACCCTAAG
* * * * * ***
2255256 TT-GGTT-CGTAGGGTTTCAT-CTCGGCTAATTC-CTTTTCTACTTAGGTTTGGCCTTGGTCACC
65 TTGGGTTGCATA--GTTTCATCCT-AGCCAACTCTCTTTT-GACTTAGGTTCCACCTTGGTCACC
* * * *
2255317 CTAAGTTTGTTCATATGGTTTCATCTCGGCCAACCTTTTTTCGACTTAGGTT
126 CTAAGTTGGTTCATATGGTTTCATCCCGGCCAACCCTTTTTCAACTTAGGTT
2255369 CTACCCTAGT
Statistics
Matches: 149, Mismatches: 23, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
196 3 0.02
197 19 0.13
198 127 0.85
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (198 bp):
GGTTTGTATGGTTTCATCTCAACCAACCCCTTTTTAACTTAGGTTTCGCCTTAGTCACCCTAAGT
TGGGTTGCATAGTTTCATCCTAGCCAACTCTCTTTTGACTTAGGTTCCACCTTGGTCACCCTAAG
TTGGTTCATATGGTTTCATCCCGGCCAACCCTTTTTCAACTTAGGTTTTGCCTTGGTCACCCTAA
GTT
Found at i:2255381 original size:132 final size:131
Alignment explanation
Indices: 2255016--2255434 Score: 427
Period size: 132 Copynumber: 3.2 Consensus size: 131
2255006 TTTATCTCAA
* *
2255016 CCAACCCCTTTT-TGACTTAGGTTTCGCCTTAGTCACCCTTAGTTGGGTTGCATA--GTTTCATC
1 CCAA-CCCTTTTCT-ACTTAGGTTTCGCCTTGGTCACCCTAAGTT-GGTT-CATATGGTTTCATC
* * * * * *
2255078 -CTAGCCAACTCTCTTTT-GACTTAGGTTCCACCTTGGTCACCTTTAGTTGGTTTGTATGGTTTC
62 TC-AGCCAAC-CTTTTTTCGACTTAGGTTCTACCTTGGTCACCGTAAGTTGGTTCGTAGGGTTTC
2255141 ATCCCGG
125 ATCCCGG
* * **
2255148 CCAACCCTTTTTCAACTTAGGTTTTGCCTTGGTCACCCTAAGTTGGTTTGTATGGTTTCATCTCA
1 CCAACCC-TTTTCTACTTAGGTTTCGCCTTGGTCACCCTAAGTTGGTTCATATGGTTTCATCTCA
* * * * *
2255213 GCCAACCCTTTTTCAACTTAGGTTTTGCCTTGGTCACCGTAAGTTGGTTCGTAGGGTTTCATCTC
65 GCCAACCTTTTTTCGACTTAGGTTCTACCTTGGTCACCGTAAGTTGGTTCGTAGGGTTTCATCCC
2255278 GG
130 GG
* * * * *
2255280 CTAATTCCTTTTCTACTTAGGTTTGGCCTTGGTCACCCTAAGTTTGTTCATATGGTTTCATCTCG
1 CCAA-CCCTTTTCTACTTAGGTTTCGCCTTGGTCACCCTAAGTTGGTTCATATGGTTTCATCTCA
* * * * * ** *
2255345 GCCAACCTTTTTTCGACTTAGGTTCTACCCTAGTCACC-AAAGTCGGTTCGCATAGTTTCGTCCC
65 GCCAACCTTTTTTCGACTTAGGTTCTACCTTGGTCACCGTAAGTTGGTTCGTAGGGTTTCATCCC
2255409 GG
130 GG
* **
2255411 CCAATCCTTTTAGACTTAGGTTTC
1 CCAACCCTTTTCTACTTAGGTTTC
2255435 ACCCTAGTCT
Statistics
Matches: 238, Mismatches: 42, Indels: 16
0.80 0.14 0.05
Matches are distributed among these distances:
130 19 0.08
131 36 0.15
132 180 0.76
133 3 0.01
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (131 bp):
CCAACCCTTTTCTACTTAGGTTTCGCCTTGGTCACCCTAAGTTGGTTCATATGGTTTCATCTCAG
CCAACCTTTTTTCGACTTAGGTTCTACCTTGGTCACCGTAAGTTGGTTCGTAGGGTTTCATCCCG
G
Found at i:2255382 original size:66 final size:65
Alignment explanation
Indices: 2254994--2255368 Score: 373
Period size: 66 Copynumber: 5.7 Consensus size: 65
2254984 CCTAACAGTA
* * * * *
2254994 GGTTTGTATGGTTTTATCTCAACCAACCCCTTTTT-GACTTAGGTTTCGCCTTAGTCACCCTTAG
1 GGTTCGTATGGTTTCATCTCAGCCAA-CCCTTTTTCGACTTAGGTTT-GCCTTGGTCACCCTAAG
2255058 TT
64 TT
* * * ** * *
2255060 GGGTT-GCATAGTTTCATC-CTAGCCAACTCTCTTTT-GACTTAGGTTCCACCTTGGTCACCTTT
1 -GGTTCGTATGGTTTCATCTC-AGCCAACCCT-TTTTCGACTTAGGTT-TGCCTTGGTCACCCTA
2255122 AGTT
62 AGTT
* * * *
2255126 GGTTTGTATGGTTTCATCCCGGCCAACCCTTTTTCAACTTAGGTTTTGCCTTGGTCACCCTAAGT
1 GGTTCGTATGGTTTCATCTCAGCCAACCCTTTTTCGACTTAGG-TTTGCCTTGGTCACCCTAAGT
2255191 T
65 T
* * *
2255192 GGTTTGTATGGTTTCATCTCAGCCAACCCTTTTTCAACTTAGGTTTTGCCTTGGTCACCGTAAGT
1 GGTTCGTATGGTTTCATCTCAGCCAACCCTTTTTCGACTTAGG-TTTGCCTTGGTCACCCTAAGT
2255257 T
65 T
* * * * *
2255258 GGTTCGTAGGGTTTCATCTCGGCTAATTCC-TTTTCTACTTAGGTTTGGCCTTGGTCACCCTAAG
1 GGTTCGTATGGTTTCATCTCAGCCAA-CCCTTTTTCGACTTAGGTTT-GCCTTGGTCACCCTAAG
2255322 TT
64 TT
* * * *
2255324 TGTTCATATGGTTTCATCTCGGCCAACCTTTTTTCGACTTAGGTT
1 GGTTCGTATGGTTTCATCTCAGCCAACCCTTTTTCGACTTAGGTT
2255369 CTACCCTAGT
Statistics
Matches: 263, Mismatches: 35, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
65 16 0.06
66 238 0.90
67 9 0.03
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (65 bp):
GGTTCGTATGGTTTCATCTCAGCCAACCCTTTTTCGACTTAGGTTTGCCTTGGTCACCCTAAGTT
Found at i:2262567 original size:73 final size:73
Alignment explanation
Indices: 2262445--2262592 Score: 251
Period size: 73 Copynumber: 2.0 Consensus size: 73
2262435 CGTCTCGTAA
* * *
2262445 AGATATTGGAACTTAACACTGACAATGAGATAGAAAAAATATGTGGAAATGCCTCATGTTTCATG
1 AGATATTGGAACTTAACAATGACAATGAGACAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
*
2262510 AAATTATG
66 AAATAATG
*
2262518 AGATATTGGAACTTAACAATGACAATGAGACAGGAAAAATATGTAGAAATGCCTCATGTTTCATG
1 AGATATTGGAACTTAACAATGACAATGAGACAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
2262583 AAATAATG
66 AAATAATG
2262591 AG
1 AG
2262593 GGAATTAACG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.27
Consensus pattern (73 bp):
AGATATTGGAACTTAACAATGACAATGAGACAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
AAATAATG
Found at i:2265026 original size:17 final size:17
Alignment explanation
Indices: 2265006--2265052 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
2264996 ATATATGTAA
2265006 AATATAAATATATATTT
1 AATATAAATATATATTT
* * *
2265023 AATATAAGTATGTGTTT
1 AATATAAATATATATTT
*
2265040 AATATTAATATAT
1 AATATAAATATAT
2265053 TTAAATTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
AATATAAATATATATTT
Found at i:2274809 original size:20 final size:20
Alignment explanation
Indices: 2274784--2274822 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2274774 CATTTCAAGC
2274784 ATGTATCAATACATTTACTT
1 ATGTATCAATACATTTACTT
*
2274804 ATGTATCAATATATTTACT
1 ATGTATCAATACATTTACT
2274823 ATTTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (20 bp):
ATGTATCAATACATTTACTT
Found at i:2281525 original size:14 final size:14
Alignment explanation
Indices: 2281508--2281545 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2281498 ATACATGATT
2281508 TTTAATTTTTACAA
1 TTTAATTTTTACAA
2281522 TTTAATCTTTT-CAA
1 TTTAAT-TTTTACAA
2281536 -TTAATTTTTA
1 TTTAATTTTTA
2281546 TGGTATAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.18
13 5 0.23
14 9 0.41
15 4 0.18
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTAATTTTTACAA
Found at i:2293738 original size:52 final size:52
Alignment explanation
Indices: 2293590--2293718 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
2293580 CGAAATATGA
* *
2293590 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTTGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
2293642 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
2293694 AAATTTGCTTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2293719 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:2293745 original size:13 final size:13
Alignment explanation
Indices: 2293727--2293751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2293717 CAAAGATCAG
2293727 TGTATCGATACAA
1 TGTATCGATACAA
2293740 TGTATCGATACA
1 TGTATCGATACA
2293752 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2293814 original size:13 final size:13
Alignment explanation
Indices: 2293796--2293847 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
2293786 AGCTTCGTAG
2293796 CGATACATTGTAT
1 CGATACATTGTAT
2293809 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
2293828 CGATACATTGTAT
1 CGATACATTGTAT
2293841 CGATACA
1 CGATACA
2293848 ATCGTTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:2294777 original size:100 final size:104
Alignment explanation
Indices: 2294618--2295080 Score: 271
Period size: 100 Copynumber: 4.8 Consensus size: 104
2294608 ATGACAATGT
* * * * * ** * *
2294618 GCTGATTCATGGCCAGCGACATTTAGACTTGAAGA--AAAATGCCAATGTGCT-AAGGCAAGGGC
1 GCTGATTCAAGGCCAACGATATTGAGACTTAAAGATGAAGGTGCCAATGTGCTGAA-TCAAGGCC
* * *
2294680 AGTGACATTGGACTTAGGAATG-TTA-AAGATGCCAATAC
65 AGTGACATTGGACTTAGGAAAGATGACAAGACGCCAATAC
* *
2294718 GCTGATTCAAGGCCAACGAT-TT-AGACTTAAGGATGAAGGTGTCAATGTGCTGAATCAAGGCCA
1 GCTGATTCAAGGCCAACGATATTGAGACTTAAAGATGAAGGTGCCAATGTGCTGAATCAAGGCCA
* * * * *
2294781 GCGACATT-GA-TT-TGAAAGATGACGAAGGCGCTAATAT
66 GTGACATTGGACTTAGGAAAGATGAC-AAGACGCCAATAC
* * * *
2294818 GTTGATTCAAGGCCAGCGATATTGGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
1 GCTGATTCAAGGCCAACGATATTGAGACTTAAAGATGAAGGTGCCAATGTGCTGAATCAAGGCCA
* * ** *
2294883 CTGACATTGGTCTT---AAAGATG---AGGTGCCAATAT
66 GTGACATTGGACTTAGGAAAGATGACAAGACGCCAATAC
* * * * * *
2294916 GCTGATTCAAAGCTAGCGATATTG-GAC-T-----T-AAGGTGCCAGTGTGCTGATTCAAGGCTA
1 GCTGATTCAAGGCCAACGATATTGAGACTTAAAGATGAAGGTGCCAATGTGCTGAATCAAGGCCA
* * * *
2294973 GCGACATTGGTCTT---AAAGA-CA-AAGGA-GCCAATAT
66 GTGACATTGGACTTAGGAAAGATGACAA-GACGCCAATAC
* *
2295007 GCTGATTCAAGGCCAGCGATATTG-GACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCA
1 GCTGATTCAAGGCCAACGATATTGAGACTTAAAGATGAAGGTGCCAATGTGCTGAATCAAGGCCA
*
2295065 GCGACATTGGACTTAG
66 GTGACATTGGACTTAG
2295081 AAGAAGACGC
Statistics
Matches: 303, Mismatches: 43, Indels: 40
0.78 0.11 0.10
Matches are distributed among these distances:
90 43 0.14
91 35 0.12
92 41 0.14
96 1 0.00
97 7 0.02
98 44 0.15
99 4 0.01
100 71 0.23
101 4 0.01
102 50 0.17
103 1 0.00
104 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (104 bp):
GCTGATTCAAGGCCAACGATATTGAGACTTAAAGATGAAGGTGCCAATGTGCTGAATCAAGGCCA
GTGACATTGGACTTAGGAAAGATGACAAGACGCCAATAC
Found at i:2294869 original size:102 final size:95
Alignment explanation
Indices: 2294712--2295089 Score: 377
Period size: 102 Copynumber: 3.9 Consensus size: 95
2294702 TTAAAGATGC
* * * * *
2294712 CAATACGCTGATTCAAGGCCAACGAT-TTAGACTTAAGGATGAAGGTGTCAATGTGCTGAATCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----AT-AAGGTGCCAATGTGCTGATTCAA
*
2294776 GGCCAGCGACATTGAT-TTGAAAGATGACGAAGGCG
61 GGCCAGCGACATTGGTCTT-AAAGATGACGAAGGCG
*
2294811 CTAATATGTTGATTCAAGGCCAGCGATATTGGGACTTAAAGATGAAGGTGCCAATGTGCTGATTC
1 C-AATATGCTGATTCAAGGCCAGCGATATT-GGACTT----AT-AAGGTGCCAATGTGCTGATTC
2294876 AAGGCCA-CTGACATTGGTCTTAAAGATGA-G--GTGC-
59 AAGGCCAGC-GACATTGGTCTTAAAGATGACGAAG-GCG
* * * *
2294910 CAATATGCTGATTCAAAGCTAGCGATATTGGAC-T-TAAGGTGCCAGTGTGCTGATTCAAGGCTA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTATAAGGTGCCAATGTGCTGATTCAAGGCCA
* *
2294973 GCGACATTGGTCTT-AA-A-GACAAAGGAG
66 GCGACATTGGTCTTAAAGATGACGAAGGCG
2295000 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGGTGCCAATGTGCTGATTCAAGGCC
1 -CAATATGCTGATTCAAGGCCAGCGATATTGGACTTATAAGGTGCCAATGTGCTGATTCAAGGCC
* *
2295064 AGCGACATTGGACTTAGAAGAAGACG
65 AGCGACATTGGTCTTA-AAGATGACG
2295090 CCACCAACTT
Statistics
Matches: 240, Mismatches: 21, Indels: 39
0.80 0.07 0.13
Matches are distributed among these distances:
87 2 0.01
88 1 0.00
89 3 0.01
90 39 0.16
91 33 0.14
92 40 0.17
94 2 0.01
95 1 0.00
96 4 0.02
97 4 0.02
98 25 0.10
99 3 0.01
100 24 0.10
101 4 0.02
102 53 0.22
103 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.24
Consensus pattern (95 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTATAAGGTGCCAATGTGCTGATTCAAGGCCA
GCGACATTGGTCTTAAAGATGACGAAGGCG
Found at i:2294922 original size:48 final size:48
Alignment explanation
Indices: 2294709--2295084 Score: 314
Period size: 48 Copynumber: 7.9 Consensus size: 48
2294699 ATGTTAAAGA
* * * * *
2294709 TGCCAATACGCTGATTCAAGGCCAACGA-TTTAGACTTAAGGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-AGG
* * * *
2294757 TGTCAATGTGCTGAATCAAGGCCAGCGACATT-GATTTGAAAGATGACGAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAAGATGA-G--G
* *
2294808 -GCGCTAATATGTTGATTCAAGGCCAGCGATATTGGGACTTAAAGATGAAGG
1 TGC-C-AATATGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATG-AGG
* *
2294859 TGCCAATGTGCTGATTCAAGGCCA-CTGACATTGGTCTTAAAGATGAGG
1 TGCCAATATGCTGATTCAAGGCCAGC-GACATTGGACTTAAAGATGAGG
* * *
2294907 TGCCAATATGCTGATTCAAAGCTAGCGATATTGGACTT----A--AGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGG
* * * * **
2294949 TGCCAGTGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-TGAGG
* *
2294998 AGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A--AGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGG
*
2295041 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA-AAGA
2295085 AGACGCCACC
Statistics
Matches: 267, Mismatches: 37, Indels: 49
0.76 0.10 0.14
Matches are distributed among these distances:
42 36 0.13
43 38 0.14
44 1 0.00
46 3 0.01
47 2 0.01
48 62 0.23
49 58 0.22
50 24 0.09
51 4 0.01
52 26 0.10
53 8 0.03
54 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (48 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGG
Found at i:2295031 original size:49 final size:48
Alignment explanation
Indices: 2294612--2295085 Score: 271
Period size: 48 Copynumber: 9.9 Consensus size: 48
2294602 CGAAGAATGA
* * * *
2294612 CAATGTGCTGATTCATGGCCAGCGACATTTAGACTTGAAGAAAA--ATGC
1 CAATATGCTGATTCAAGGCCAGCGACA-TTGGACTTAAAGAAAAGGA-GC
* * ** * * *
2294660 CAATGTGCTAAGGCAAGGGCAGTGACATTGGACTTAGGAATGTTAAA-GATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTA--AA-G-AAAAGGA-GC
* * * * * * * *
2294712 CAATACGCTGATTCAAGGCCAACGA-TTTAGACTTAAGGATGAAGGTGT
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-AAAGGAGC
* * * *
2294760 CAATGTGCTGAATCAAGGCCAGCGACATT-GATTTGAAAGATGACGAAGGCGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAAGA--A--AAGGAGC
* * * * *
2294812 TAATATGTTGATTCAAGGCCAGCGATATTGGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGA-AAAGGAGC
* * ** *
2294862 CAATGTGCTGATTCAAGGCCA-CTGACATTGGTCTTAAAGATGAGGTGC
1 CAATATGCTGATTCAAGGCCAGC-GACATTGGACTTAAAGAAAAGGAGC
* * * *
2294910 CAATATGCTGATTCAAAGCTAGCGATATTGGACTT------AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGAGC
* * * *
2294952 CAGTGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGACAAAGGAGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-AAAGGAGC
* *
2295001 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-----AAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGAGC
*
2295044 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAGAAGAA
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTA-AAGAA
2295086 GACGCCACCA
Statistics
Matches: 326, Mismatches: 71, Indels: 57
0.72 0.16 0.13
Matches are distributed among these distances:
42 36 0.11
43 40 0.12
47 7 0.02
48 84 0.26
49 59 0.18
50 30 0.09
51 11 0.03
52 50 0.15
53 5 0.02
54 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGAGC
Found at i:2295113 original size:27 final size:28
Alignment explanation
Indices: 2295086--2295140 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
2295076 CTTAGAAGAA
*
2295086 GACGCCACCAACTTGTGTGCTTTTGAAG
1 GACGCCACCAACTTGTGGGCTTTTGAAG
** **
2295114 GTTGCCACTGACTTGTGGGCTTTTGAA
1 GACGCCACCAACTTGTGGGCTTTTGAA
2295141 AAGGGTGCCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (28 bp):
GACGCCACCAACTTGTGGGCTTTTGAAG
Found at i:2295127 original size:28 final size:29
Alignment explanation
Indices: 2295096--2295165 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 29
2295086 GACGCCACCA
* *
2295096 ACTTGTGTGCTTTTG-AAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAGGGTGCCACTG
2295124 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTG-AAAGGGTGCCACTG
2295154 ACTTGTGGGCTT
1 ACTTGTGGGCTT
2295166 AAAAGGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 14 0.37
30 24 0.63
ACGTcount: A:0.16, C:0.17, G:0.31, T:0.36
Consensus pattern (29 bp):
ACTTGTGGGCTTTTGAAAGGGTGCCACTG
Found at i:2295217 original size:34 final size:34
Alignment explanation
Indices: 2295138--2295218 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
2295128 GTGGGCTTTT
*
2295138 GAAAAGGGTGCCACTGACTTGTGGGCTTAAAAGGAA
1 GAAAA-GGTGCCACGGACTTGTGGGCTTAAAA-GAA
*
2295174 -AAATA-GTGCCACGGAGTTGTGGGCTTACAAA-AA
1 GAAA-AGGTGCCACGGACTTGTGGGCTTA-AAAGAA
2295207 GAAAAGGTGCCA
1 GAAAAGGTGCCA
2295219 ATATGCTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
33 3 0.08
34 29 0.74
35 6 0.15
36 1 0.03
ACGTcount: A:0.36, C:0.15, G:0.31, T:0.19
Consensus pattern (34 bp):
GAAAAGGTGCCACGGACTTGTGGGCTTAAAAGAA
Found at i:2295327 original size:33 final size:32
Alignment explanation
Indices: 2295260--2295341 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 32
2295250 TTAAAGGTGT
* *
2295260 CACGGAGTTGTGGACTTAAAAAGAAAAGGCGC
1 CACGGAGTTGTGGGCTTAAAAAGAAAAGACGC
* * *
2295292 CACGGAGTTATGGGCTTAAAAGGAAAAAGATGC
1 CACGGAGTTGTGGGCTTAAAAAG-AAAAGACGC
* *
2295325 CACAGACTTGTGGGCTT
1 CACGGAGTTGTGGGCTT
2295342 TTGAAGGTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 20 0.49
33 21 0.51
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (32 bp):
CACGGAGTTGTGGGCTTAAAAAGAAAAGACGC
Found at i:2295363 original size:28 final size:28
Alignment explanation
Indices: 2295320--2295405 Score: 111
Period size: 28 Copynumber: 3.0 Consensus size: 28
2295310 AAAGGAAAAA
*
2295320 GATGCCACAGACTTGTGGGCTTTTGAAG
1 GATGCCACTGACTTGTGGGCTTTTGAAG
* * *
2295348 GTTGCCACTGATTTGTGGGC-TTTGAAAAA
1 GATGCCACTGACTTGTGGGCTTTTG--AAG
2295377 GATGCCACTGACTTGTGGGCTTTTGAAG
1 GATGCCACTGACTTGTGGGCTTTTGAAG
2295405 G
1 G
2295406 GTGAGGAATG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
27 4 0.08
28 20 0.42
29 20 0.42
30 4 0.08
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.31
Consensus pattern (28 bp):
GATGCCACTGACTTGTGGGCTTTTGAAG
Found at i:2295392 original size:29 final size:29
Alignment explanation
Indices: 2295314--2295399 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
2295304 GGCTTAAAAG
*
2295314 GAAAAAGATGCCACAGACTTGTGGGCTTTT
1 GAAAAAGATGCCACTGACTTGTGGGC-TTT
* * *
2295344 G--AAGGTTGCCACTGATTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
2295371 GAAAAAGATGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
2295400 TGAAGGGTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 4 0.09
28 19 0.40
29 23 0.49
30 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.30
Consensus pattern (29 bp):
GAAAAAGATGCCACTGACTTGTGGGCTTT
Found at i:2296841 original size:16 final size:16
Alignment explanation
Indices: 2296822--2296875 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
2296812 ATCCGGACCC
2296822 TTTTTG-TTGTTGTTT
1 TTTTTGTTTGTTGTTT
2296837 TTTTTGTTTGTTGTTT
1 TTTTTGTTTGTTGTTT
* *
2296853 TTTTATCTTTTTTGTATT
1 TTTT-TGTTTGTTGT-TT
2296871 TTTTT
1 TTTTT
2296876 CTTCTCTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 6 0.18
16 13 0.38
17 9 0.26
18 6 0.18
ACGTcount: A:0.04, C:0.02, G:0.13, T:0.81
Consensus pattern (16 bp):
TTTTTGTTTGTTGTTT
Found at i:2296875 original size:22 final size:24
Alignment explanation
Indices: 2296836--2296887 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
2296826 TGTTGTTGTT
* *
2296836 TTTTTTGTTTGTTGTTTTTTTATC
1 TTTTTTGTATGTTGTTTTCTTATC
*
2296860 TTTTTTGTAT-TT-TTTTCTTCTC
1 TTTTTTGTATGTTGTTTTCTTATC
2296882 TTTTTT
1 TTTTTT
2296888 TTTGGAGGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 14 0.56
23 2 0.08
24 9 0.36
ACGTcount: A:0.04, C:0.08, G:0.08, T:0.81
Consensus pattern (24 bp):
TTTTTTGTATGTTGTTTTCTTATC
Found at i:2296878 original size:17 final size:16
Alignment explanation
Indices: 2296828--2296878 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
2296818 ACCCTTTTTG
*
2296828 TTGTTGTTTTTTTTGT
1 TTGTTGTTTTTTTTCT
2296844 TTGTTGTTTTTTTATCT
1 TTGTTGTTTTTTT-TCT
*
2296861 TTTTTGTATTTTTTTCT
1 TTGTTGT-TTTTTTTCT
2296878 T
1 T
2296879 CTCTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 13 0.42
17 12 0.39
18 6 0.19
ACGTcount: A:0.04, C:0.04, G:0.12, T:0.80
Consensus pattern (16 bp):
TTGTTGTTTTTTTTCT
Found at i:2306386 original size:21 final size:21
Alignment explanation
Indices: 2306360--2306430 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
2306350 TATCCAAATA
2306360 TATCGATACATTTGTAGAATG
1 TATCGATACATTTGTAGAATG
2306381 TATCGATACATTTGTAGAATG
1 TATCGATACATTTGTAGAATG
*
2306402 TATCAATACATTTGTAGAATG
1 TATCGATACATTTGTAGAATG
2306423 TATCGATA
1 TATCGATA
2306431 TAAGGTCCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (21 bp):
TATCGATACATTTGTAGAATG
Found at i:2306486 original size:19 final size:19
Alignment explanation
Indices: 2306462--2306523 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
2306452 TTTTGAACTT
2306462 CAAACAGTTTGTATCGATA
1 CAAACAGTTTGTATCGATA
**
2306481 CAAACAGAAAATGTATCGATA
1 CAAACAG--TTTGTATCGATA
*
2306502 CATA-AGTGTTGTATCGATA
1 CAAACAGT-TTGTATCGATA
2306521 CAA
1 CAA
2306524 TGTATCGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (19 bp):
CAAACAGTTTGTATCGATA
Found at i:2306529 original size:13 final size:13
Alignment explanation
Indices: 2306511--2306535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2306501 ACATAAGTGT
2306511 TGTATCGATACAA
1 TGTATCGATACAA
2306524 TGTATCGATACA
1 TGTATCGATACA
2306536 TAAATTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2306531 original size:32 final size:32
Alignment explanation
Indices: 2306490--2306560 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
2306480 ACAAACAGAA
*
2306490 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAATGTTGTATCGATAC
*
2306522 AATGTATCGATACATAAATTTTGTATCGATAC
1 AATGTATCGATACATAAATGTTGTATCGATAC
2306554 AATGTAT
1 AATGTAT
2306561 TGCTACGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (32 bp):
AATGTATCGATACATAAATGTTGTATCGATAC
Found at i:2306548 original size:19 final size:18
Alignment explanation
Indices: 2306492--2306554 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
2306482 AAACAGAAAA
*
2306492 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAAT-T
2306511 TGTATCGATAC---AA--
1 TGTATCGATACATAAATT
2306524 TGTATCGATACATAAATTT
1 TGTATCGATACATAAA-TT
2306543 TGTATCGATACA
1 TGTATCGATACA
2306555 ATGTATTGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
16 3 0.08
19 23 0.62
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAATT
Found at i:2306605 original size:21 final size:21
Alignment explanation
Indices: 2306579--2306621 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2306569 AGCTACTGCC
2306579 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
*
2306600 AAGGAAATGTATTGATACATT
1 AAGGAAATGTATCGATACATT
2306621 A
1 A
2306622 TATCGATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:2307497 original size:12 final size:12
Alignment explanation
Indices: 2307480--2307506 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2307470 GCTCATCTGC
2307480 TGGCCAGATATG
1 TGGCCAGATATG
2307492 TGGCCAGATATG
1 TGGCCAGATATG
2307504 TGG
1 TGG
2307507 TTAGGCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.15, G:0.37, T:0.26
Consensus pattern (12 bp):
TGGCCAGATATG
Found at i:2308003 original size:38 final size:38
Alignment explanation
Indices: 2307927--2308003 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
2307917 ACACTTGACA
* * * *
2307927 ATAATATTAAGATATTTATTACCAATCAATATATATCT
1 ATAATAGTAAGATAATTATTACCAATCAATACACATCT
**
2307965 ATAATAGTAAGATAATTATTATTAATCAATACACATCT
1 ATAATAGTAAGATAATTATTACCAATCAATACACATCT
2308003 A
1 A
2308004 ATAAAACACT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (38 bp):
ATAATAGTAAGATAATTATTACCAATCAATACACATCT
Found at i:2308064 original size:2 final size:2
Alignment explanation
Indices: 2308057--2308091 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2308047 TGAAGTACAA
2308057 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2308092 AAATACAAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2310712 original size:18 final size:18
Alignment explanation
Indices: 2310689--2310724 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2310679 TGCAAGTTTC
2310689 GAGGAAGTTGTGCTAATG
1 GAGGAAGTTGTGCTAATG
*
2310707 GAGGAAGTTGTGTTAATG
1 GAGGAAGTTGTGCTAATG
2310725 TGCACACAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.39, T:0.31
Consensus pattern (18 bp):
GAGGAAGTTGTGCTAATG
Found at i:2311003 original size:6 final size:6
Alignment explanation
Indices: 2310994--2311021 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2310984 AACATTTATT
2310994 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
2311022 TATCGAGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:2314098 original size:18 final size:18
Alignment explanation
Indices: 2314054--2314105 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
2314044 AACAAAATAA
*
2314054 TATTTAATTATTTGTTATTT
1 TATTTAA-TATTT-TAATTT
*
2314074 T-TATAATATTTTAATTT
1 TATTTAATATTTTAATTT
2314091 TATTTAATATTTTAA
1 TATTTAATATTTTAA
2314106 AATTTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 6 0.21
18 17 0.61
19 4 0.14
20 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TATTTAATATTTTAATTT
Found at i:2322977 original size:27 final size:27
Alignment explanation
Indices: 2322939--2322991 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
2322929 TTTAAAGGAG
2322939 TCCCATAAGTTACAAATCCTATCCTAA
1 TCCCATAAGTTACAAATCCTATCCTAA
*
2322966 TCCCATAAGTTACAAATTCTATCCTA
1 TCCCATAAGTTACAAATCCTATCCTA
2322992 TTCATAACCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (27 bp):
TCCCATAAGTTACAAATCCTATCCTAA
Found at i:2325944 original size:15 final size:14
Alignment explanation
Indices: 2325920--2325950 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2325910 CCCCCAAAAC
2325920 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
2325934 AAAAGAAAAAAGAAA
1 AAAA-AAAAAAGAAA
2325949 AA
1 AA
2325951 TCTCTCCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:2328364 original size:13 final size:12
Alignment explanation
Indices: 2328344--2328454 Score: 50
Period size: 12 Copynumber: 8.9 Consensus size: 12
2328334 GATTAATATC
2328344 TATT-TATTTTA
1 TATTATATTTTA
2328355 TCATTATATTTTA
1 T-ATTATATTTTA
*
2328368 TATTTTATTTATA
1 TATTATATTT-TA
2328381 TAAATTATATTTT-
1 T--ATTATATTTTA
* * *
2328394 TAATAAATTTAA
1 TATTATATTTTA
* *
2328406 AATAATATTTT-
1 TATTATATTTTA
*
2328417 TATT-TTTATTTA
1 TATTATAT-TTTA
*
2328429 TATTTTATTTATA
1 TATTATATTT-TA
2328442 TAAATTATATTTT
1 T--ATTATATTTT
2328455 TAATAAGATC
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
10 2 0.03
11 13 0.18
12 23 0.32
13 17 0.23
14 2 0.03
15 16 0.22
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:2328382 original size:20 final size:20
Alignment explanation
Indices: 2328296--2328393 Score: 55
Period size: 19 Copynumber: 5.2 Consensus size: 20
2328286 TCAGCGTAAA
*
2328296 TTTATTT-TA-ATTTTATGT
1 TTTATTTATATATTTTATAT
*
2328314 TTTTTTTA-ATATTTT-TAT
1 TTTATTTATATATTTTATAT
* * * * *
2328332 ATGATTAATATCTATT-TAT
1 TTTATTTATATATTTTATAT
*
2328351 TTTA-TCATTATATTTTATAT
1 TTTATTTA-TATATTTTATAT
**
2328371 TTTATTTATATAAATTATAT
1 TTTATTTATATATTTTATAT
2328391 TTT
1 TTT
2328394 TAATAAATTT
Statistics
Matches: 58, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
18 15 0.26
19 21 0.36
20 20 0.34
21 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTATTTATATATTTTATAT
Found at i:2328499 original size:61 final size:60
Alignment explanation
Indices: 2328373--2328509 Score: 152
Period size: 61 Copynumber: 2.2 Consensus size: 60
2328363 TTTTATATTT
* * *
2328373 TATTTATATAAATTATATTTTTAATAAATTTAAAATAATATTTTTATTTTTATTTATATTT
1 TATTTATATAAATTATATTTTTAATAAATTTAAAATAATATTTTTA-TTTTATATAAATTA
* * *
2328434 TATTTATATAAATTATATTTTTAATAAGATCATTATATTTATA-TTTTA-TTTATATAAATTA
1 TATTTATATAAATTATATTTTTAATAA-AT--TTAAAATAATATTTTTATTTTATATAAATTA
*
2328495 TATTTTTAATAAATT
1 TATTTAT-ATAAATT
2328510 TAAAATAATA
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
61 43 0.66
62 9 0.14
63 5 0.08
64 8 0.12
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (60 bp):
TATTTATATAAATTATATTTTTAATAAATTTAAAATAATATTTTTATTTTATATAAATTA
Found at i:2328532 original size:46 final size:45
Alignment explanation
Indices: 2328428--2328528 Score: 143
Period size: 46 Copynumber: 2.2 Consensus size: 45
2328418 ATTTTTATTT
* * *
2328428 ATATTTTATTTATATAAATTATATTTTTAATAAGATCATTATATTT
1 ATATTTTATTTATATAAATTATATTTTTAATAAGAT-ATTAAAATA
2328474 ATATTTTATTTATATAAATTATATTTTTAATAA-AT-TTAAAATA
1 ATATTTTATTTATATAAATTATATTTTTAATAAGATATTAAAATA
2328517 ATATTTTTATTT
1 ATA-TTTTATTT
2328529 TTATTTAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
43 8 0.16
44 8 0.16
45 2 0.04
46 33 0.65
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (45 bp):
ATATTTTATTTATATAAATTATATTTTTAATAAGATATTAAAATA
Found at i:2328603 original size:16 final size:16
Alignment explanation
Indices: 2328549--2328621 Score: 58
Period size: 16 Copynumber: 4.3 Consensus size: 16
2328539 ATAAAAATAT
* *
2328549 ATAAATATTAATATAAA
1 ATAAATTTTAA-ATTAA
*
2328566 ATAATATTTTAAAAATATA
1 ATAA-ATTTT-AAATTA-A
2328585 ATAAATTTTAAATTAA
1 ATAAATTTTAAATTAA
*
2328601 ATAGA-TTTAAATTTAA
1 ATAAATTTTAAA-TTAA
2328617 ATAAA
1 ATAAA
2328622 AAAATAAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
15 6 0.13
16 13 0.28
17 9 0.20
18 11 0.24
19 7 0.15
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (16 bp):
ATAAATTTTAAATTAA
Found at i:2328997 original size:2 final size:2
Alignment explanation
Indices: 2328990--2329051 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
2328980 AAGATCATAA
* *
2328990 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2329032 AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
2329052 TTTCTGGTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2329120 original size:2 final size:2
Alignment explanation
Indices: 2329113--2329141 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2329103 CTAAACTTTC
2329113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2329142 TGTTAATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2329357 original size:20 final size:20
Alignment explanation
Indices: 2329312--2329348 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
2329302 TAAATTTATG
2329312 AAATATGAAAATAATATAAT
1 AAATATGAAAATAATATAAT
*
2329332 AAATATG-ATATAATATA
1 AAATATGAAAATAATATA
2329349 TTTAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATATGAAAATAATATAAT
Found at i:2339651 original size:185 final size:185
Alignment explanation
Indices: 2339362--2339740 Score: 564
Period size: 185 Copynumber: 2.0 Consensus size: 185
2339352 TTTCATAATG
* *
2339362 TATCGATACATGCATTTGAAATTTATATCTATTTGACGCATTGTATTGATACTTTTCACTCTGTA
1 TATCGATACATGCATTTGAAATTTATATCTAGTTGACGCATTGTATTGATACTTTTCACTATGTA
* *
2339427 TCAACACAATGTACCATGTATCGATACAAACAATGGTAGGGTAGGTACTGCAAGTTTCATGTATC
66 TCAACACAATGTACCATGTATCGATACAAACAATGGTAGGGTAGCTACTACAAGTTTCATGTATC
* * *
2339492 GATACAATTCGTTGTGTATCGATACCAAGATCATGTATCGATACTTTTAAGTCTA
131 GATACAATTCGTTATGTATCGATACCAAGATCACGTATCGATACTTCTAAGTCTA
* * * *
2339547 TATCAATACATGCATTTGAAATTTATATC-CGTTG-GGCATAATGTATTGATGCTTTTCACTATG
1 TATCGATACATGCATTTGAAATTTATATCTAGTTGACGCAT--TGTATTGATACTTTTCACTATG
* * * * * *
2339610 TATCGATACAATGTACCTTGTATCGATACAAATAATGGTAGGGTAGCTATTACTAGTTTCATGTA
64 TATCAACACAATGTACCATGTATCGATACAAACAATGGTAGGGTAGCTACTACAAGTTTCATGTA
*
2339675 TCGATACAATTCGTTATGTATCGATACCAAGATCACGTATCGATACTTCTAAGTCTG
129 TCGATACAATTCGTTATGTATCGATACCAAGATCACGTATCGATACTTCTAAGTCTA
2339732 TATCGATAC
1 TATCGATAC
2339741 TATCTAGGGT
Statistics
Matches: 173, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
183 4 0.02
184 3 0.02
185 166 0.96
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (185 bp):
TATCGATACATGCATTTGAAATTTATATCTAGTTGACGCATTGTATTGATACTTTTCACTATGTA
TCAACACAATGTACCATGTATCGATACAAACAATGGTAGGGTAGCTACTACAAGTTTCATGTATC
GATACAATTCGTTATGTATCGATACCAAGATCACGTATCGATACTTCTAAGTCTA
Found at i:2350611 original size:19 final size:20
Alignment explanation
Indices: 2350595--2350655 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 20
2350585 AATATTAATA
2350595 TAAATTT-ATTTATTTAAAT
1 TAAATTTAATTTATTTAAAT
2350614 TAAATTTAATTTA---AAAT
1 TAAATTTAATTTATTTAAAT
2350631 ATAAATCTTAAATTTTATTTAAAT
1 -TAAAT-TT-AA-TTTATTTAAAT
2350655 T
1 T
2350656 TATCAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
17 4 0.12
18 5 0.15
19 9 0.26
20 7 0.21
21 4 0.12
23 1 0.03
24 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAATTTAATTTATTTAAAT
Found at i:2350743 original size:17 final size:16
Alignment explanation
Indices: 2350704--2350749 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
2350694 GCTTATTTAT
* *
2350704 ATTATATTTTTTTATA
1 ATTATATTTTTTAAAA
2350720 ATT-TATTTTTTAAAA
1 ATTATATTTTTTAAAA
*
2350735 A-TATATATTTTAAAA
1 ATTATATTTTTTAAAA
2350750 TTTAATCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 1 0.04
15 22 0.85
16 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATATTTTTTAAAA
Found at i:2351007 original size:18 final size:20
Alignment explanation
Indices: 2350986--2351027 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2350976 TTAATTTTAT
2350986 ATTTAA-ATTTTT-TTTAAA
1 ATTTAATATTTTTATTTAAA
*
2351004 ATTTAATATTTTTATTTAAT
1 ATTTAATATTTTTATTTAAA
2351024 ATTT
1 ATTT
2351028 TTAAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 6 0.29
20 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTAATATTTTTATTTAAA
Found at i:2351057 original size:18 final size:20
Alignment explanation
Indices: 2351026--2351062 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
2351016 TATTTAATAT
2351026 TTTTAAATTATTAAATAAAA
1 TTTTAAATTATTAAATAAAA
2351046 TTTTAAA-T-TTAAATAAA
1 TTTTAAATTATTAAATAAA
2351063 TAAGTTCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTAAATTATTAAATAAAA
Found at i:2352366 original size:10 final size:10
Alignment explanation
Indices: 2352351--2352395 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
2352341 TTCTATCAAC
2352351 AAAAAAAGAA
1 AAAAAAAGAA
2352361 AAAAAAAGAA
1 AAAAAAAGAA
*
2352371 AGAAAAAAGGAG
1 A-AAAAAA-GAA
2352383 AAAAAAAGAA
1 AAAAAAAGAA
2352393 AAA
1 AAA
2352396 TTATGTATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 16 0.52
11 12 0.39
12 3 0.10
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:2352386 original size:22 final size:22
Alignment explanation
Indices: 2352351--2352393 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2352341 TTCTATCAAC
2352351 AAAAAAAGAAAAAAAAAGAAAG
1 AAAAAAAGAAAAAAAAAGAAAG
* *
2352373 AAAAAAGGAGAAAAAAAGAAA
1 AAAAAAAGAAAAAAAAAGAAA
2352394 AATTATGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAAAAAAAAAGAAAG
Found at i:2353254 original size:32 final size:33
Alignment explanation
Indices: 2353217--2353282 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
2353207 TCGTTACATT
*
2353217 TTTTATATAAATATTTATATATTAATA-ATTTA
1 TTTTATATAAATATTTACATATTAATATATTTA
*
2353249 TTTTATATAAATATTTACATATTTATATATTTA
1 TTTTATATAAATATTTACATATTAATATATTTA
2353282 T
1 T
2353283 ATCATGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 25 0.81
33 6 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (33 bp):
TTTTATATAAATATTTACATATTAATATATTTA
Found at i:2353255 original size:18 final size:18
Alignment explanation
Indices: 2353228--2353265 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2353218 TTTATATAAA
*
2353228 TATTTATATATTAATAATT
1 TATTTATATATAAAT-ATT
2353247 TATTT-TATATAAATATT
1 TATTTATATATAAATATT
2353264 TA
1 TA
2353266 CATATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTATATATAAATATT
Found at i:2353282 original size:8 final size:8
Alignment explanation
Indices: 2353227--2353284 Score: 55
Period size: 8 Copynumber: 7.2 Consensus size: 8
2353217 TTTTATATAA
2353227 ATATTTAT
1 ATATTTAT
*
2353235 ATATTAAT
1 ATATTTAT
2353243 A-ATTTATT
1 ATATTTA-T
* * *
2353251 TTATATAA
1 ATATTTAT
*
2353259 ATATTTAC
1 ATATTTAT
2353267 ATATTTAT
1 ATATTTAT
2353275 ATATTTAT
1 ATATTTAT
2353283 AT
1 AT
2353285 CATGTTTATA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
7 4 0.10
8 31 0.79
9 4 0.10
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
ATATTTAT
Found at i:2353340 original size:24 final size:27
Alignment explanation
Indices: 2353289--2353342 Score: 78
Period size: 24 Copynumber: 2.1 Consensus size: 27
2353279 TTATATCATG
2353289 TTTATATTATTTTTGTATCATATTATAT
1 TTTATATTATTTTTGTA-CATATTATAT
2353317 TTTA-ATTATTTTT-TA-ATATTATAT
1 TTTATATTATTTTTGTACATATTATAT
2353341 TT
1 TT
2353343 ATGTTATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 11 0.42
26 2 0.08
27 9 0.35
28 4 0.15
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTATATTATTTTTGTACATATTATAT
Found at i:2353349 original size:24 final size:26
Alignment explanation
Indices: 2353289--2353349 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 26
2353279 TTATATCATG
2353289 TTTATATTATTTTTGTATCATATTATA
1 TTTATATTATTTTTGTA-CATATTATA
2353316 TTT-TAATTATTTTT-TA-ATATTATA
1 TTTAT-ATTATTTTTGTACATATTATA
*
2353340 TTTATGTTAT
1 TTTATATTAT
2353350 GTCTTAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 15 0.48
25 1 0.03
26 3 0.10
27 12 0.39
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTATATTATTTTTGTACATATTATA
Found at i:2353411 original size:27 final size:24
Alignment explanation
Indices: 2353367--2353454 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 24
2353357 TTTATCTTAT
*
2353367 ATTTTATATAACATTTTATATAATTAA
1 ATTTTAAATAA-A-TTTAT-TAATTAA
*
2353394 ATTTTAAATTTAAATTTATTTATTAAA
1 ATTTTAAA--TAAATTTATTAATT-AA
2353421 TATTTTTAAATAAATTGTATTAATTATA
1 -A-TTTTAAATAAATT-TATTAATTA-A
2353449 ATTTTA
1 ATTTTA
2353455 TTTAATTAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
26 9 0.18
27 22 0.43
28 10 0.20
29 10 0.20
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (24 bp):
ATTTTAAATAAATTTATTAATTAA
Found at i:2353426 original size:43 final size:46
Alignment explanation
Indices: 2353379--2353476 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 46
2353369 TTTATATAAC
*
2353379 ATTTTATATAATTAAATT-T-TAAATT-TAAATTTATTT-ATTAAAT
1 ATTTTATA-AATTAAATTGTATAAATTATAAATTTATTTAATTAAAA
* *
2353422 ATTTT-TAAA-TAAATTGTATTAATTATAATTTTATTTAATTAAAA
1 ATTTTATAAATTAAATTGTATAAATTATAAATTTATTTAATTAAAA
2353466 ATTTTATAAAT
1 ATTTTATAAAT
2353477 ATTAAACCTC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
40 6 0.13
41 3 0.07
42 7 0.15
43 15 0.33
44 11 0.24
45 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (46 bp):
ATTTTATAAATTAAATTGTATAAATTATAAATTTATTTAATTAAAA
Found at i:2353863 original size:22 final size:22
Alignment explanation
Indices: 2353833--2353874 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2353823 ACATGTAATA
2353833 ATTTAATATAAATTA-ATTAAAT
1 ATTTAATAT-AATTACATTAAAT
*
2353855 ATTTTATATAATTACATTAA
1 ATTTAATATAATTACATTAA
2353875 TTTATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTAATATAATTACATTAAAT
Found at i:2354561 original size:46 final size:46
Alignment explanation
Indices: 2354504--2354598 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
2354494 TAAGTGATTT
* *
2354504 AATTTATTAA-TTATA-AAAATTTAATAATATAATTTGATAAAATTAA
1 AATTTATTAATTTATATAAAAATTAATAATA-AATTTAAT-AAATTAA
* * *
2354550 AATTTTTTAATTTATATAAAAATTAATACTAAATTTAATAATTTAA
1 AATTTATTAATTTATATAAAAATTAATAATAAATTTAATAAATTAA
2354596 AAT
1 AAT
2354599 ATAAATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
46 18 0.43
47 12 0.29
48 12 0.29
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (46 bp):
AATTTATTAATTTATATAAAAATTAATAATAAATTTAATAAATTAA
Found at i:2356948 original size:19 final size:20
Alignment explanation
Indices: 2356904--2356953 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
2356894 ATTTATATCA
2356904 AAAATTAATTAAATAGTAAT
1 AAAATTAATTAAATAGTAAT
**
2356924 TTAATT-ATTAAA-ATGTAAT
1 AAAATTAATTAAATA-GTAAT
2356943 AAAATTTAATT
1 AAAA-TTAATT
2356954 TAAAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
18 1 0.04
19 13 0.57
20 6 0.26
21 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
AAAATTAATTAAATAGTAAT
Found at i:2356960 original size:17 final size:17
Alignment explanation
Indices: 2356940--2356999 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
2356930 ATTAAAATGT
2356940 AATAAAATTTAATTTAA
1 AATAAAATTTAATTTAA
* *
2356957 AATAAAATATAA-AT-A
1 AATAAAATTTAATTTAA
* *
2356972 AATAAAATTTTATTAAA
1 AATAAAATTTAATTTAA
*
2356989 AATATAATTTA
1 AATAAAATTTA
2357000 GCTTAATTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 11 0.33
16 1 0.03
17 21 0.64
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAAATTTAATTTAA
Found at i:2356988 original size:15 final size:15
Alignment explanation
Indices: 2356940--2356988 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
2356930 ATTAAAATGT
2356940 AATAAAATTTAATTTAA
1 AATAAAATTTAA-TT-A
* *
2356957 AATAAAATATAAATA
1 AATAAAATTTAATTA
*
2356972 AATAAAATTTTATTA
1 AATAAAATTTAATTA
2356987 AA
1 AA
2356989 AATATAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 15 0.56
16 1 0.04
17 11 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATAAAATTTAATTA
Found at i:2362123 original size:10 final size:10
Alignment explanation
Indices: 2362108--2362137 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2362098 TTATGTGCAT
2362108 GTGGAGTGGG
1 GTGGAGTGGG
*
2362118 GTGGAGTGGA
1 GTGGAGTGGG
2362128 GTGGAGTGGG
1 GTGGAGTGGG
2362138 TTCCACAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.67, T:0.20
Consensus pattern (10 bp):
GTGGAGTGGG
Found at i:2368427 original size:14 final size:14
Alignment explanation
Indices: 2368408--2368448 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
2368398 TTTTCATGGA
*
2368408 TTAATTGTTTATTC
1 TTAATTATTTATTC
2368422 TTAATTATTTATTC
1 TTAATTATTTATTC
2368436 TTAATTATCTTAT
1 TTAATTAT-TTAT
2368449 GCTATGGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.63
Consensus pattern (14 bp):
TTAATTATTTATTC
Found at i:2382050 original size:5 final size:5
Alignment explanation
Indices: 2382036--2382075 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
2382026 GAGGGAAACT
* *
2382036 AGGGA GGGGA AGGGA AGGGA AGGGA AGGGA ATGG- AGGGA A
1 AGGGA AGGGA AGGGA AGGGA AGGGA AGGGA AGGGA AGGGA A
2382076 AAGGGGGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 3 0.10
5 27 0.90
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.03
Consensus pattern (5 bp):
AGGGA
Found at i:2387109 original size:30 final size:30
Alignment explanation
Indices: 2386995--2387110 Score: 144
Period size: 30 Copynumber: 3.8 Consensus size: 30
2386985 GAAGCCTATG
* *
2386995 TACCTAAATTATGATGCATATCCAAATTAGA
1 TACCTAAATTGTGATGCATATCCAAA-AAGA
* * *
2387026 TACCTAAATTGCGATACATAT-AAAAAATGA
1 TACCTAAATTGTGATGCATATCCAAAAA-GA
*
2387056 TACCTAAATTGTGATGCACATCCAAAAAGA
1 TACCTAAATTGTGATGCATATCCAAAAAGA
*
2387086 TACCTAAATTGGGATGCATATCCAA
1 TACCTAAATTGTGATGCATATCCAA
2387111 CTAGACAATA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.01
30 48 0.67
31 23 0.32
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (30 bp):
TACCTAAATTGTGATGCATATCCAAAAAGA
Found at i:2390382 original size:5 final size:5
Alignment explanation
Indices: 2390372--2390398 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2390362 CAGAGATCAA
2390372 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
2390399 GCATGGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2392711 original size:13 final size:13
Alignment explanation
Indices: 2392693--2392717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2392683 ATTTAAAGTC
2392693 TATTAAGTTTATT
1 TATTAAGTTTATT
2392706 TATTAAGTTTAT
1 TATTAAGTTTAT
2392718 AAGATTGTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TATTAAGTTTATT
Found at i:2396157 original size:40 final size:40
Alignment explanation
Indices: 2396113--2396211 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 40
2396103 AATAGTTACT
*
2396113 AACATATTTGAAAATTCAA-CTTTACCCCTAATTAGTTGCA
1 AACATATTTGAAAATTCAATC-TTAACCCTAATTAGTTGCA
* ** * *
2396153 AACATGTTTGAAAATTCAATCTTAATTCTAATTGGTTGGA
1 AACATATTTGAAAATTCAATCTTAACCCTAATTAGTTGCA
**
2396193 AACATCGTTGAAAATTCAA
1 AACATATTTGAAAATTCAA
2396212 GCATTAACAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
40 49 0.98
41 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.35
Consensus pattern (40 bp):
AACATATTTGAAAATTCAATCTTAACCCTAATTAGTTGCA
Found at i:2399548 original size:13 final size:13
Alignment explanation
Indices: 2399530--2399558 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2399520 AACCCTTGTA
2399530 TATATCGATACAT
1 TATATCGATACAT
2399543 TATATCGATACAT
1 TATATCGATACAT
2399556 TAT
1 TAT
2399559 GTTTGTATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (13 bp):
TATATCGATACAT
Found at i:2399674 original size:33 final size:32
Alignment explanation
Indices: 2399637--2399699 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
2399627 CCACTGTTTG
2399637 TATCGATACATG-GCACATTGTATCGATACAATA
1 TATCGATACATGAG-A-ATTGTATCGATACAATA
2399670 TATCGATACATGAAGAATTGTATCGATACA
1 TATCGATACATG-AGAATTGTATCGATACA
2399700 TTGTCCCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (32 bp):
TATCGATACATGAGAATTGTATCGATACAATA
Found at i:2401230 original size:20 final size:20
Alignment explanation
Indices: 2401206--2401281 Score: 98
Period size: 20 Copynumber: 3.7 Consensus size: 20
2401196 TTTCACAATT
*
2401206 TGTATCGATACATTGTTCAT
1 TGTATCGATACATTGTTCAA
* *
2401226 TGTATCGATACATCTGGGTAAA
1 TGTATCGATACAT-T-GTTCAA
*
2401248 TGTATCGATACATTTTTCAA
1 TGTATCGATACATTGTTCAA
2401268 TGTATCGATACATT
1 TGTATCGATACATT
2401282 CAAGCATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 30 0.62
21 2 0.04
22 16 0.33
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTGTTCAA
Found at i:2403267 original size:28 final size:28
Alignment explanation
Indices: 2403233--2403303 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
2403223 TCATCTCGCG
2403233 GATACTCCAACCTCGTTATTTCATCGGA
1 GATACTCCAACCTCGTTATTTCATCGGA
* *
2403261 GATACTCCAACCTTGTTATTTCATCGGG
1 GATACTCCAACCTCGTTATTTCATCGGA
2403289 GATACTCCAACCTCG
1 GATACTCCAACCTCG
2403304 ATTTTATTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (28 bp):
GATACTCCAACCTCGTTATTTCATCGGA
Found at i:2403353 original size:79 final size:78
Alignment explanation
Indices: 2403255--2403479 Score: 319
Period size: 79 Copynumber: 2.8 Consensus size: 78
2403245 TCGTTATTTC
*
2403255 ATCGGAGATACTCCAACCTTGTTATTTCATCGGGGATACTCCAACCTCGATTTTA-TTTCTAAAA
1 ATCGGAGATACTCCAACCTTGTTATTTCA-AGGGGATACTCCAACCTCGATTTTATTTTC-AAAA
2403319 CACTAATTTTTCACA
64 CACTAATTTTTCACA
* * * *
2403334 ATCGGGGATACTCTAACCTTGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAAC
1 ATCGGAGATACTCCAACCTTGTTATTT-CAAGGGGATACTCCAACCTCGATTTTATTTTCAAAAC
2403399 ACTAATTTTTCACA
65 ACTAATTTTTCACA
* **
2403413 ATCAGAGATACTCCAACCCCGTTAATTTCAAGGGGATACTCCAA-CTCCGATTTTATTTTCAAAA
1 ATCGGAGATACTCCAACCTTGTT-ATTTCAAGGGGATACTCCAACCT-CGATTTTATTTTCAAAA
2403477 CAC
64 CAC
2403480 CGATTTTCCA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
78 1 0.01
79 120 0.92
80 9 0.07
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (78 bp):
ATCGGAGATACTCCAACCTTGTTATTTCAAGGGGATACTCCAACCTCGATTTTATTTTCAAAACA
CTAATTTTTCACA
Found at i:2406109 original size:32 final size:33
Alignment explanation
Indices: 2406051--2406113 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
2406041 TATCCAGATG
* *
2406051 TATCGATACATTATGCTTTGTATCGATACATTA
1 TATCGATACATGATGCATTGTATCGATACATTA
2406084 TATCGATACATGAT-CATTGTATCGATACAT
1 TATCGATACATGATGCATTGTATCGATACAT
2406114 GTACAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (33 bp):
TATCGATACATGATGCATTGTATCGATACATTA
Found at i:2406124 original size:20 final size:19
Alignment explanation
Indices: 2406029--2406133 Score: 73
Period size: 20 Copynumber: 5.7 Consensus size: 19
2406019 AACCCTTGTA
*
2406029 TGTATCGATACAT-ATCCAGA
1 TGTATCGATACATGAT-CA-T
* *
2406049 TGTATCGATACATTATGCTT
1 TGTATCGATACATGAT-CAT
2406069 TGTATCGATACAT--T-A-
1 TGTATCGATACATGATCAT
2406084 --TATCGATACATGATCAT
1 TGTATCGATACATGATCAT
2406101 TGTATCGATACATG-TACAAT
1 TGTATCGATACATGAT-C-AT
*
2406121 TGTATTGATACAT
1 TGTATCGATACAT
2406134 ATCGATACAT
Statistics
Matches: 71, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
13 11 0.15
15 1 0.01
16 1 0.01
18 2 0.03
19 13 0.18
20 40 0.56
21 3 0.04
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:2408389 original size:75 final size:71
Alignment explanation
Indices: 2408206--2408547 Score: 359
Period size: 71 Copynumber: 4.7 Consensus size: 71
2408196 GTATTAAAAT
* *
2408206 TTTTTTAGGATATTATTTATCTTTATTTATAAAAGTTTAAATTTTTTTTGGGTATGATTATACT-
1 TTTTTTAGG-TATAATTTATCTTTATTTATAAAAGTTTAAATTTTTTTTAGGTATGATTATA-TG
*
2408270 AGTTAAAA
64 AGTTTAAA
* *
2408278 TTTTTGAGGTATAATCTATCTTTATTTATAAAAGTTTAAATGTGTTTTTTAGGTAT-ACTTATAT
1 TTTTTTAGGTATAATTTATCTTTATTTATAAAAGTTTAAAT-T-TTTTTTAGGTATGA-TTATAT
2408342 GAGTTTAAA
63 GAGTTTAAA
* * * *
2408351 TTTTTTATGGTTATAATTTATTTTTATTTGTAGAAGTTTAAATATATTTTTTAGATATGATTATA
1 TTTTTTA-GG-TATAATTTATCTTTATTTATAAAAGTTTAAAT-T-TTTTTTAGGTATGATTATA
* *
2408416 CGAGTTTATA
62 TGAGTTTAAA
* * * * * * *
2408426 TTTTTAATTGTATAATTCATTTTTATTTGTAAAAATTTAAATTTATTTTTGGGT-TGATTATATG
1 TTTTTTA-GGTATAATTTATCTTTATTTATAAAAGTTTAAATTT-TTTTTAGGTATGATTATATG
2408490 AGTTTAAA
64 AGTTTAAA
* *
2408498 -TTTTTAGGGTATTATTTATCTTTATTTTTAAAAGTTTAAATTTTTATTTA
1 TTTTTTA-GGTATAATTTATCTTTATTTATAAAAGTTTAAATTTTT-TTTA
2408548 AAAGTTACAA
Statistics
Matches: 228, Mismatches: 33, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
70 2 0.01
71 68 0.30
72 28 0.12
73 37 0.16
74 31 0.14
75 61 0.27
76 1 0.00
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.55
Consensus pattern (71 bp):
TTTTTTAGGTATAATTTATCTTTATTTATAAAAGTTTAAATTTTTTTTAGGTATGATTATATGAG
TTTAAA
Found at i:2409475 original size:20 final size:20
Alignment explanation
Indices: 2409450--2409489 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2409440 TTTACTAATA
*
2409450 TATTTTT-TTGTATTATATAG
1 TATTTTTATT-TAATATATAG
2409470 TATTTTTATTTAATATATAG
1 TATTTTTATTTAATATATAG
2409490 CTTCTAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (20 bp):
TATTTTTATTTAATATATAG
Found at i:2412137 original size:21 final size:22
Alignment explanation
Indices: 2412071--2412158 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 22
2412061 ATTTTAACTC
**
2412071 AAAATTATTAATAAATAATTAATT
1 AAAATT-TTAATATTTAATT-ATT
* *
2412095 AAAATTTTTTATAATTAAAATTATT
1 AAAA-TTTTAAT-ATT-TAATTATT
*
2412120 AAATTTTTAAT-TTTAATTATT
1 AAAATTTTAATATTTAATTATT
2412141 AAAATTTTAATATTTAAT
1 AAAATTTTAATATTTAAT
2412159 CAATAAATCT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
21 17 0.33
22 8 0.15
24 14 0.27
25 9 0.17
26 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATTTTAATATTTAATTATT
Found at i:2412157 original size:15 final size:15
Alignment explanation
Indices: 2412093--2412157 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
2412083 AAATAATTAA
* *
2412093 TTAAAATTTTTTATAA
1 TTAAAA-TTTTAATAT
2412109 TTAAAATTATTAA-AT
1 TTAAAATT-TTAATAT
**
2412124 TTTTAATTTTAAT-T
1 TTAAAATTTTAATAT
2412138 ATTAAAATTTTAATAT
1 -TTAAAATTTTAATAT
2412154 TTAA
1 TTAA
2412158 TCAATAAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.13
15 24 0.62
16 10 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAAATTTTAATAT
Found at i:2412165 original size:22 final size:21
Alignment explanation
Indices: 2412119--2412165 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2412109 TTAAAATTAT
* * *
2412119 TAAATTTTTAATTTTAATTAT
1 TAAAATTTTAATTTTAATCAA
2412140 TAAAATTTTAATATTTAATCAA
1 TAAAATTTTAAT-TTTAATCAA
2412162 TAAA
1 TAAA
2412166 TCTGCTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAAATTTTAATTTTAATCAA
Found at i:2412302 original size:18 final size:17
Alignment explanation
Indices: 2412281--2412318 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2412271 TCATATTTTA
2412281 TTTTTATTTTTAATTAAT
1 TTTTTATTTTTAATT-AT
*
2412299 TTTTTATTTTTTATTAT
1 TTTTTATTTTTAATTAT
2412316 TTT
1 TTT
2412319 CTCAAAGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTATTTTTAATTAT
Found at i:2412857 original size:7 final size:7
Alignment explanation
Indices: 2412841--2412879 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
2412831 AAAGATAAAA
*
2412841 AAATTAT
1 AAATTTT
*
2412848 AAATATT
1 AAATTTT
2412855 AAATTTT
1 AAATTTT
2412862 AAATTTT
1 AAATTTT
2412869 AAATTTAT
1 AAATTT-T
2412877 AAA
1 AAA
2412880 ATATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
7 24 0.86
8 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
AAATTTT
Found at i:2412864 original size:14 final size:14
Alignment explanation
Indices: 2412841--2412885 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2412831 AAAGATAAAA
*
2412841 AAATTATAAATATT
1 AAATTTTAAATATT
*
2412855 AAATTTTAAATTTT
1 AAATTTTAAATATT
2412869 AAATTTATAAAATATT
1 AAATTT-T-AAATATT
2412885 A
1 A
2412886 TTATTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 18 0.69
15 1 0.04
16 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTTTAAATATT
Found at i:2413572 original size:56 final size:57
Alignment explanation
Indices: 2413512--2413622 Score: 152
Period size: 57 Copynumber: 2.0 Consensus size: 57
2413502 TAAAACTAAT
* *
2413512 TTAATTTCATACTTTCAT-AATTTTTTATATAATTTATATTAGTTTAATCAAAATGC
1 TTAATTTCACACCTTCATCAATTTTTTATATAATTTATATTAGTTTAATCAAAATGC
* * * * *
2413568 TTAATTTTACACCTTCGTCATTTTTTTGTATAATTTATATTTGTTTAATCAAAAT
1 TTAATTTCACACCTTCATCAATTTTTTATATAATTTATATTAGTTTAATCAAAAT
2413623 ATTGCATTCC
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
56 14 0.30
57 33 0.70
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.53
Consensus pattern (57 bp):
TTAATTTCACACCTTCATCAATTTTTTATATAATTTATATTAGTTTAATCAAAATGC
Found at i:2413931 original size:2 final size:2
Alignment explanation
Indices: 2413926--2413953 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2413916 TATTTTTTTA
2413926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2413954 TAATGGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2419759 original size:18 final size:18
Alignment explanation
Indices: 2419738--2419791 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
2419728 AAAATAATAT
2419738 ATATTTATATAAATTTTA
1 ATATTTATATAAATTTTA
2419756 ATATATTA-AT-AA-TTT-
1 ATAT-TTATATAAATTTTA
2419771 AT-TTTATATAAATTTTA
1 ATATTTATATAAATTTTA
2419788 ATAT
1 ATAT
2419792 ATACTTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
13 3 0.10
14 3 0.10
15 4 0.13
16 6 0.20
17 4 0.13
18 7 0.23
19 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTTATATAAATTTTA
Found at i:2419759 original size:20 final size:20
Alignment explanation
Indices: 2419736--2419793 Score: 60
Period size: 13 Copynumber: 3.3 Consensus size: 20
2419726 TTAAAATAAT
2419736 ATATATTTATATAAATTTTA
1 ATATATTTATATAAATTTTA
2419756 ATATA-TTA-AT-AA--TT-
1 ATATATTTATATAAATTTTA
2419770 -TAT-TTTATATAAATTTTA
1 ATATATTTATATAAATTTTA
2419788 ATATAT
1 ATATAT
2419794 ACTTATATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
13 6 0.20
14 2 0.07
15 4 0.13
17 4 0.13
18 2 0.07
19 6 0.20
20 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATTTATATAAATTTTA
Found at i:2419781 original size:32 final size:33
Alignment explanation
Indices: 2419698--2419793 Score: 113
Period size: 32 Copynumber: 2.8 Consensus size: 33
2419688 ATTCATAATT
* * *
2419698 TATATATTTTTATATATTATAAATATATTTAAAATAA
1 TATATATTTATATAAATT-TTAATATA-TT--AATAA
2419735 TATATATTTATATAAATTTTAATATATTAATAA
1 TATATATTTATATAAATTTTAATATATTAATAA
*
2419768 TTTAT-TTTATATAAATTTTAATATAT
1 TATATATTTATATAAATTTTAATATAT
2419794 ACTTATATTG
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
32 21 0.38
33 9 0.16
35 2 0.04
36 7 0.13
37 16 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TATATATTTATATAAATTTTAATATATTAATAA
Found at i:2419792 original size:14 final size:14
Alignment explanation
Indices: 2419743--2419794 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
2419733 AATATATATT
2419743 TATATAAATTTTAA
1 TATATAAATTTTAA
**
2419757 TATATTAATAATTTATTT
1 TATA-T-A-AATTT-TAA
2419775 TATATAAATTTTAA
1 TATATAAATTTTAA
2419789 TATATA
1 TATATA
2419795 CTTATATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 11 0.37
15 6 0.20
16 2 0.07
17 6 0.20
18 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:2419794 original size:16 final size:16
Alignment explanation
Indices: 2419743--2419794 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2419733 AATATATATT
2419743 TATATAAATTTTAATA
1 TATATAAATTTTAATA
* * *
2419759 TAT-TAATAATTTATTT
1 TATATAA-ATTTTAATA
2419775 TATATAAATTTTAATA
1 TATATAAATTTTAATA
2419791 TATA
1 TATA
2419795 CTTATATTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 3 0.11
16 22 0.79
17 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATAAATTTTAATA
Found at i:2419822 original size:23 final size:21
Alignment explanation
Indices: 2419796--2419853 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
2419786 TAATATATAC
2419796 TTATATTGAATTAATATTATTTT
1 TTATATT-AATTAA-ATTATTTT
* *
2419819 TTAT-TATATTTTAATTATTTT
1 TTATAT-TAATTAAATTATTTT
2419840 TTATATT-ATTAAAT
1 TTATATTAATTAAAT
2419854 ATAATAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 5 0.17
21 13 0.45
22 6 0.21
23 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTATATTAATTAAATTATTTT
Found at i:2419830 original size:11 final size:10
Alignment explanation
Indices: 2419810--2419843 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2419800 ATTGAATTAA
2419810 TATTATTTTT
1 TATTATTTTT
2419820 TATTATATTTT
1 TATTAT-TTTT
*
2419831 AATTATTTTT
1 TATTATTTTT
2419841 TAT
1 TAT
2419844 ATTATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TATTATTTTT
Found at i:2420117 original size:17 final size:17
Alignment explanation
Indices: 2420086--2420125 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2420076 ATTTATCTGT
*
2420086 ATAAAA-AATAATTAAA
1 ATAAAATAAAAATTAAA
*
2420102 ATAAAATAAAAATTAAT
1 ATAAAATAAAAATTAAA
2420119 ATAAAAT
1 ATAAAAT
2420126 TTATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAATAAAAATTAAA
Found at i:2420131 original size:21 final size:21
Alignment explanation
Indices: 2420089--2420142 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
2420079 TATCTGTATA
*
2420089 AAAAATAAT-TAAAATAAAAT
1 AAAAATAATATAAAATAATAT
*
2420109 AAAAATTAATATAAAAT-TTAT
1 AAAAA-TAATATAAAATAATAT
2420130 AAAAAT-ATATAAA
1 AAAAATAATATAAA
2420143 TATGTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 7 0.23
20 6 0.20
21 11 0.37
22 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATAATATAAAATAATAT
Found at i:2420133 original size:20 final size:19
Alignment explanation
Indices: 2420110--2420161 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
2420100 AAATAAAATA
*
2420110 AAAATTAATATAAA-ATTTAT
1 AAAATT-ATATAAATATGT-T
*
2420130 AAAAATATATAAATATGTT
1 AAAATTATATAAATATGTT
2420149 AAAATTTATATAA
1 AAAA-TTATATAA
2420162 TATAATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAATTATATAAATATGTT
Found at i:2420179 original size:31 final size:30
Alignment explanation
Indices: 2420120--2420208 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 30
2420110 AAAATTAATA
*
2420120 TAAAATTTATA-AAAAT-ATATAAATATGT
1 TAAAATTTATATAATATAATATAAATATGT
*
2420148 TAAAATTTATATAATATAATTATTAATATGT
1 TAAAATTTATATAATATAA-TATAAATATGT
*
2420179 TAAAATTTTTATAA-AT-ATAT-AATAT-T
1 TAAAATTTATATAATATAATATAAATATGT
2420205 TAAA
1 TAAA
2420209 CATAATTATA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
26 5 0.09
27 5 0.09
28 14 0.25
29 5 0.09
30 3 0.05
31 23 0.42
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (30 bp):
TAAAATTTATATAATATAATATAAATATGT
Found at i:2420217 original size:27 final size:26
Alignment explanation
Indices: 2420158--2420219 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
2420148 TAAAATTTAT
*
2420158 ATAA-TATAATTATTAATATGTTAAA
1 ATAATTATAAATATTAATATGTTAAA
**
2420183 ATTTTTATAAATATATAATAT-TTAAA
1 ATAATTATAAATAT-TAATATGTTAAA
2420209 CATAATTATAA
1 -ATAATTATAA
2420220 CATAAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 2 0.07
26 13 0.45
27 14 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
ATAATTATAAATATTAATATGTTAAA
Found at i:2420742 original size:13 final size:13
Alignment explanation
Indices: 2420724--2420748 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2420714 GTATTTTTTT
2420724 TAAAAAAATAATA
1 TAAAAAAATAATA
2420737 TAAAAAAATAAT
1 TAAAAAAATAAT
2420749 TTTTTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAAAATAATA
Found at i:2424092 original size:24 final size:24
Alignment explanation
Indices: 2424073--2424122 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
2424063 TATTTTTAGG
2424073 AAACTA-AAATTTAAATTTTTTAAA
1 AAACTATAAA-TTAAATTTTTTAAA
*
2424097 AAACTATAAATTAAA-TATTTAAA
1 AAACTATAAATTAAATTTTTTAAA
2424120 AAA
1 AAA
2424123 TAGAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
24 11 0.46
25 3 0.12
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
AAACTATAAATTAAATTTTTTAAA
Found at i:2424163 original size:27 final size:27
Alignment explanation
Indices: 2424132--2424243 Score: 81
Period size: 27 Copynumber: 4.1 Consensus size: 27
2424122 ATAGAAAAAG
2424132 AAAATTTTCATTTTTAAT-TATATTTTA
1 AAAATTTTCATTTTTAATATAT-TTTTA
2424159 AAAATTTATCAAAATTTTT-ATATATTTTTA
1 AAAATTT-TC---ATTTTTAATATATTTTTA
* *
2424189 AAAATTTTAAATTTTAA-AT-TTTTATA
1 AAAATTTTCATTTTTAATATATTTT-TA
* * *
2424215 TAATTTTTACATTTTTAA-ATTTTTTTA
1 AAAATTTT-CATTTTTAATATATTTTTA
2424242 AA
1 AA
2424244 CTATTTAGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
25 4 0.06
26 15 0.22
27 20 0.29
28 6 0.09
29 1 0.01
30 14 0.20
31 9 0.13
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (27 bp):
AAAATTTTCATTTTTAATATATTTTTA
Found at i:2424213 original size:34 final size:34
Alignment explanation
Indices: 2424170--2424237 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
2424160 AAATTTATCA
2424170 AAATTTTTATAT-ATTTTTAAAAATTTTAAATTTT
1 AAATTTTTATATAATTTTT-AAAATTTTAAATTTT
* *
2424204 AAATTTTTATATAATTTTTACATTTTTAAATTTT
1 AAATTTTTATATAATTTTTAAAATTTTAAATTTT
2424238 TTTAAACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 25 0.81
35 6 0.19
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (34 bp):
AAATTTTTATATAATTTTTAAAATTTTAAATTTT
Found at i:2424228 original size:8 final size:8
Alignment explanation
Indices: 2424170--2424238 Score: 59
Period size: 8 Copynumber: 8.0 Consensus size: 8
2424160 AAATTTATCA
2424170 AAATTTTT
1 AAATTTTT
2424178 ATATATTTTT
1 A-A-ATTTTT
*
2424188 AAAAATTTT
1 -AAATTTTT
2424197 AAA-TTTT
1 AAATTTTT
2424204 AAATTTTTAT
1 AAA-TTTT-T
2424214 ATAATTTTT
1 A-AATTTTT
*
2424223 ACATTTTT
1 AAATTTTT
2424231 AAATTTTT
1 AAATTTTT
2424239 TTAAACTATT
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
7 7 0.14
8 17 0.33
9 11 0.22
10 13 0.25
11 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (8 bp):
AAATTTTT
Found at i:2424871 original size:16 final size:16
Alignment explanation
Indices: 2424828--2424874 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2424818 TGAGTTCAGG
*
2424828 TCATTTCAGATTCGGG
1 TCATTTCAGATTCGGA
* * *
2424844 TTATTGCGGATTCGGA
1 TCATTTCAGATTCGGA
2424860 TCATTTCAGATTCGG
1 TCATTTCAGATTCGG
2424875 GTCAATCAGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (16 bp):
TCATTTCAGATTCGGA
Found at i:2431403 original size:12 final size:12
Alignment explanation
Indices: 2431386--2431410 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2431376 GTGAAATAAC
2431386 AGTAATTATAGG
1 AGTAATTATAGG
2431398 AGTAATTATAGG
1 AGTAATTATAGG
2431410 A
1 A
2431411 AATTAGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
AGTAATTATAGG
Found at i:2437742 original size:2 final size:2
Alignment explanation
Indices: 2437732--2437787 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
2437722 AAACCATTAA
*
2437732 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2437774 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
2437788 CACGGGCTGG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2438969 original size:12 final size:12
Alignment explanation
Indices: 2438952--2439009 Score: 75
Period size: 12 Copynumber: 4.8 Consensus size: 12
2438942 GAGAAGAAAT
2438952 TGAAAAGAAAAA
1 TGAAAAGAAAAA
2438964 TGAAAA-AAAAA
1 TGAAAAGAAAAA
*
2438975 GGGAAAAGAAAAA
1 -TGAAAAGAAAAA
2438988 TGAAAA-AAAAA
1 TGAAAAGAAAAA
2438999 TGAAAAAGAAA
1 TG-AAAAGAAA
2439010 GGAAAAACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
11 12 0.30
12 20 0.50
13 8 0.20
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (12 bp):
TGAAAAGAAAAA
Found at i:2438973 original size:11 final size:11
Alignment explanation
Indices: 2438952--2439016 Score: 76
Period size: 11 Copynumber: 5.6 Consensus size: 11
2438942 GAGAAGAAAT
2438952 TGAAAAGAAAAA
1 TGAAAA-AAAAA
2438964 TGAAAAAAAAA
1 TGAAAAAAAAA
*
2438975 GGGAAAAGAAAAA
1 -TGAAAA-AAAAA
2438988 TGAAAAAAAAA
1 TGAAAAAAAAA
*
2438999 TGAAAAAGAAA
1 TGAAAAAAAAA
*
2439010 GGAAAAA
1 TGAAAAA
2439017 CATACAGGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
11 26 0.55
12 16 0.34
13 5 0.11
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.06
Consensus pattern (11 bp):
TGAAAAAAAAA
Found at i:2438985 original size:24 final size:24
Alignment explanation
Indices: 2438953--2439009 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
2438943 AGAAGAAATT
2438953 GAAAAGAAAAATGAAAAAAAAAGG
1 GAAAAGAAAAATGAAAAAAAAAGG
*
2438977 GAAAAGAAAAATGAAAAAAAAATG
1 GAAAAGAAAAATGAAAAAAAAAGG
*
2439001 AAAAAGAAA
1 GAAAAGAAA
2439010 GGAAAAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (24 bp):
GAAAAGAAAAATGAAAAAAAAAGG
Found at i:2438998 original size:35 final size:38
Alignment explanation
Indices: 2438943--2439016 Score: 109
Period size: 35 Copynumber: 2.0 Consensus size: 38
2438933 ATATAAACAG
*
2438943 AGAAGAAATTGAAAAGAAAAATGAAAAAAAAAGGGAAA
1 AGAAGAAATTGAAAAGAAAAATGAAAAAAAAAGGAAAA
*
2438981 AGAA-AAA-TGAAAA-AAAAATGAAAAAGAAAGGAAAA
1 AGAAGAAATTGAAAAGAAAAATGAAAAAAAAAGGAAAA
2439016 A
1 A
2439017 CATACAGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 21 0.62
36 6 0.18
37 3 0.09
38 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (38 bp):
AGAAGAAATTGAAAAGAAAAATGAAAAAAAAAGGAAAA
Found at i:2439881 original size:13 final size:11
Alignment explanation
Indices: 2439855--2439887 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2439845 AATTTAGTTA
2439855 ATTTTTAAATT
1 ATTTTTAAATT
2439866 ATTTTT-AATT
1 ATTTTTAAATT
*
2439876 ATTATTAAATT
1 ATTTTTAAATT
2439887 A
1 A
2439888 AATTCTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTTTAAATT
Found at i:2439891 original size:16 final size:16
Alignment explanation
Indices: 2439872--2439903 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2439862 AATTATTTTT
2439872 AATTATTATTAAATTA
1 AATTATTATTAAATTA
*
2439888 AATTCTTATTAAATTA
1 AATTATTATTAAATTA
2439904 TTTTAATTCA
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTATTATTAAATTA
Found at i:2439951 original size:43 final size:44
Alignment explanation
Indices: 2439903--2439990 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
2439893 TTATTAAATT
**
2439903 ATTTTAATTCAAAA-TGAAAATAAAAAATATATAAGAAATAAAA
1 ATTTTAATTCAAAACAAAAAATAAAAAATATATAAGAAATAAAA
* *
2439946 ATTTTAATTTAAAACAAAAAATGAAAAATATATAAGAAATAAAA
1 ATTTTAATTCAAAACAAAAAATAAAAAATATATAAGAAATAAAA
2439990 A
1 A
2439991 AAATTATGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 13 0.32
44 27 0.68
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (44 bp):
ATTTTAATTCAAAACAAAAAATAAAAAATATATAAGAAATAAAA
Found at i:2440584 original size:15 final size:15
Alignment explanation
Indices: 2440543--2440586 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2440533 TTATATAATT
2440543 ATATTTGAATATTTAA
1 ATATTTGAAT-TTTAA
* * *
2440559 TTTTTTTAATTTTAA
1 ATATTTGAATTTTAA
2440574 ATATTTGAATTTT
1 ATATTTGAATTTT
2440587 TTAAATAGGA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (15 bp):
ATATTTGAATTTTAA
Done.