Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold491
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: 232955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:688 original size:21 final size:21
Alignment explanation
Indices: 655--699 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
645 TTGCAAGTTG
*
655 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
677 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
697 AAA
1 AAA
700 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2522 original size:15 final size:15
Alignment explanation
Indices: 2502--2532 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2492 TAAAAAAGTC
*
2502 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2517 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2532 C
1 C
2533 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:4629 original size:13 final size:13
Alignment explanation
Indices: 4611--4649 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4601 ACATTTTTCT
4611 TTGTATCGATACA
1 TTGTATCGATACA
*
4624 TTGTATCTATACA
1 TTGTATCGATACA
4637 TTGTATCGATACA
1 TTGTATCGATACA
4650 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:8022 original size:44 final size:44
Alignment explanation
Indices: 7959--8286 Score: 276
Period size: 44 Copynumber: 7.5 Consensus size: 44
7949 TAAGCTTTCA
**
7959 AGAAAGGAGGCAGATTTGACTAGGGTGGTAACCATATGTCAAAC
1 AGAAAGGAGGCAGATTTGACTAGGGTGGTAACCATACATCAAAC
* *
8003 AGAAAGGAGGCATATTTGACTAGGGTGGTAACCATACGTCAAAC
1 AGAAAGGAGGCAGATTTGACTAGGGTGGTAACCATACATCAAAC
* *
8047 AGGAAGGAGGTAGATTTGACTAGGGTGGTAACCATACATCATAGA-
1 AGAAAGGAGGCAGATTTGACTAGGGTGGTAACCATACATCA-A-AC
* * *
8092 AG-AAGGAGACAGATTTGATTAGGGTGGTAACTATACATCAAATC
1 AGAAAGGAGGCAGATTTGACTAGGGTGGTAACCATACATCAAA-C
* ** * * *
8136 A-AAATGA-AAAGAATCTAACTAGGGTGGTAACCATACATCAGAC
1 AGAAAGGAGGCAG-ATTTGACTAGGGTGGTAACCATACATCAAAC
* * * **
8179 ATGAAA-GAGACAGATTTGACCATGGTGGTAACCATATGTCAAATC
1 A-GAAAGGAGGCAGATTTGACTAGGGTGGTAACCATACATCAAA-C
* ** * * * *
8224 A-AAATGA-AAAGAATCTAACCAGGGTGGTAACCATACATCAGAC
1 AGAAAGGAGGCAG-ATTTGACTAGGGTGGTAACCATACATCAAAC
*
8267 AAGAAA-GAGGTAGATTTGAC
1 -AGAAAGGAGGCAGATTTGAC
8287 CCCATACGTT
Statistics
Matches: 233, Mismatches: 36, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
42 1 0.00
43 13 0.06
44 202 0.87
45 16 0.07
46 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (44 bp):
AGAAAGGAGGCAGATTTGACTAGGGTGGTAACCATACATCAAAC
Found at i:8287 original size:88 final size:87
Alignment explanation
Indices: 7975--8689 Score: 609
Period size: 88 Copynumber: 8.2 Consensus size: 87
7965 GAGGCAGATT
** * * *
7975 TGACTAGGGTGGTAACCATATGTCAAAC-AGAAAGGAGGCATATTTGACTAGGGTGGTAACCATA
1 TGACTAGGGTGGTAACCATACATCAGACAAGAAA-GAGGCAGATTTGACCA-GGTGGTAACCATA
* * * ** *
8039 CGTCAAA-CAGGAAGGAGGTAG-ATT
64 TGTCAAATCA-AAATGA-AAAGAATC
* * * * ** * *
8063 TGACTAGGGTGGTAACCATACATCATAGAAGAAGGAGACAGATTTGATTAGGGTGGTAACTATAC
1 TGACTAGGGTGGTAACCATACATCAGACAAGAAAGAGGCAGATTTGACCA-GGTGGTAACCATAT
*
8128 ATCAAATCAAAATGAAAAGAATC
65 GTCAAATCAAAATGAAAAGAATC
* * *
8151 TAACTAGGGTGGTAACCATACATCAGACATGAAAGAGACAGATTTGACCATGGTGGTAACCATAT
1 TGACTAGGGTGGTAACCATACATCAGACAAGAAAGAGGCAGATTTGACCA-GGTGGTAACCATAT
8216 GTCAAATCAAAATGAAAAGAATC
65 GTCAAATCAAAATGAAAAGAATC
* * * *
8239 TAACCAGGGTGGTAACCATACATCAGACAAGAAAGAGGTAGATTTGACC---------CCATACG
1 TGACTAGGGTGGTAACCATACATCAGACAAGAAAGAGGCAGATTTGACCAGGTGGTAACCATATG
* *** *
8295 TTAAATTGGATTGAAAAGAATC
66 TCAAATCAAAATGAAAAGAATC
* * * * * * * **
8317 TGACTAAGGAGGTAGCCCTACCTCAGACTAGAAAAAAACAGATTTGACCAAGGTGGTAACCATAT
1 TGACTAGGGTGGTAACCATACATCAGACAAGAAAGAGGCAGATTTGACC-AGGTGGTAACCATAT
*
8382 ATCAAATCAAAATGAAAAGAATC
65 GTCAAATCAAAATGAAAAGAATC
** * * *
8405 TGA-TCAGGGTGGTAACCA-ATGTCAGACAGGAAAGAGGCAGATTTGACTAGAGTCGTAACCATA
1 TGACT-AGGGTGGTAACCATACATCAGACAAGAAAGAGGCAGATTTGACCAG-GTGGTAACCATA
8468 TGTCAAATCAAAATGAAAAGAATC
64 TGTCAAATCAAAATGAAAAGAATC
* * ** * *
8492 TGACCAAGGTGGTAACCATATGTCAGAC-AGAAGAGAGGCAGATTTGACTAGGGTGGTAACCGTA
1 TGACTAGGGTGGTAACCATACATCAGACAAGAA-AGAGGCAGATTTGACCA-GGTGGTAACCATA
**
8556 CATCAAATCAAAATGAAAAGAATC
64 TGTCAAATCAAAATGAAAAGAATC
* * * *
8580 TGACTAGGGTGGTAACCATACGTCAGA-TAGAAGAGAGGTAGATTTGGCCATATGGT-GTAACCA
1 TGACTAGGGTGGTAACCATACATCAGACAAGAA-AGAGGCAGATTTGACC--A-GGTGGTAACCA
* *
8643 TATGCCAAATCGAAATGAAAAGAATC
62 TATGTCAAATCAAAATGAAAAGAATC
* *
8669 TAACTATGGTGGTAACCATAC
1 TGACTAGGGTGGTAACCATAC
8690 GTTAGATAGG
Statistics
Matches: 515, Mismatches: 90, Indels: 43
0.79 0.14 0.07
Matches are distributed among these distances:
78 60 0.12
86 2 0.00
87 77 0.15
88 318 0.62
89 54 0.10
90 4 0.01
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (87 bp):
TGACTAGGGTGGTAACCATACATCAGACAAGAAAGAGGCAGATTTGACCAGGTGGTAACCATATG
TCAAATCAAAATGAAAAGAATC
Found at i:8418 original size:44 final size:44
Alignment explanation
Indices: 8368--8688 Score: 221
Period size: 44 Copynumber: 7.3 Consensus size: 44
8358 ATTTGACCAA
*
8368 GGTGGTAACCATATATCAAATCAAAATGAAAAGAATCTGA-TCAG
1 GGTGGTAACCATATGTCAAATCAAAATGAAAAGAATCTGACT-AG
* ** *
8412 GGTGGTAACCA-ATGTCAGA-CAGGAAA-GAGGCAG-ATTTGACTAG
1 GGTGGTAACCATATGTCAAATCA--AAATGA-AAAGAATCTGACTAG
* * * *
8455 AGTCGTAACCATATGTCAAATCAAAATGAAAAGAATCTGACCAA
1 GGTGGTAACCATATGTCAAATCAAAATGAAAAGAATCTGACTAG
* * * * *
8499 GGTGGTAACCATATGTCAGA-CAGAA-GAGAGGCAGATTTGACTAG
1 GGTGGTAACCATATGTCAAATCAAAATGAAAAG-A-ATCTGACTAG
* **
8543 GGTGGTAACCGTACATCAAATCAAAATGAAAAGAATCTGACTAG
1 GGTGGTAACCATATGTCAAATCAAAATGAAAAGAATCTGACTAG
* * * * * * * *
8587 GGTGGTAACCATACGTCAGAT-AGAA-GAGAGGTAGATTTGGCCATAT
1 GGTGGTAACCATATGTCAAATCAAAATGAAAAG-A-ATCT-GAC-TAG
* * * *
8633 GGT-GTAACCATATGCCAAATCGAAATGAAAAGAATCTAACTAT
1 GGTGGTAACCATATGTCAAATCAAAATGAAAAGAATCTGACTAG
8676 GGTGGTAACCATA
1 GGTGGTAACCATA
8689 CGTTAGATAG
Statistics
Matches: 209, Mismatches: 49, Indels: 38
0.71 0.17 0.13
Matches are distributed among these distances:
42 10 0.05
43 44 0.21
44 113 0.54
45 26 0.12
46 12 0.06
47 4 0.02
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (44 bp):
GGTGGTAACCATATGTCAAATCAAAATGAAAAGAATCTGACTAG
Found at i:8791 original size:48 final size:48
Alignment explanation
Indices: 8704--9000 Score: 326
Period size: 48 Copynumber: 6.2 Consensus size: 48
8694 GATAGGAAAA
* * * *
8704 AAAAGAGTTTGACGAGTCCCT-ACACCAATACAATCAAACGAGGGGTG
1 AAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAACGAGGGATG
8751 AAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAACGAGGGATG
1 AAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAACGAGGGATG
* * *
8799 AAAAGAGTTTGACTAGGCCCTAACACCAATATAGTCAAACGAGGGAAG
1 AAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAACGAGGGATG
*** * * * *
8847 ATTTGAGTTTGACCAGGCCCTGACACCAATACAGTCAAAAGAAGGAAG
1 AAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAACGAGGGATG
*** * * * * *
8895 ATTTGAGTTTTACTAGGCCCTAATACCAATATAGTCAAACAAGGGATG
1 AAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAACGAGGGATG
* * * * * *
8943 AAAAGAGTTTAACCAAGCCTTAACACCGATACAGTCAAATGAAGGATG
1 AAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAACGAGGGATG
*
8991 AAAATAGTTT
1 AAAAGAGTTT
9001 AACCGAGTAG
Statistics
Matches: 211, Mismatches: 38, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
47 19 0.09
48 192 0.91
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (48 bp):
AAAAGAGTTTGACCAGGCCCTAACACCAATACAGTCAAACGAGGGATG
Found at i:8841 original size:96 final size:96
Alignment explanation
Indices: 8704--9000 Score: 362
Period size: 96 Copynumber: 3.1 Consensus size: 96
8694 GATAGGAAAA
* * * * *
8704 AAAAGAGTTTGACGAGTCCCT-ACACCAATACAATCAAACGAGGGGTGAAAAGAGTTTGACCAGG
1 AAAAGAGTTTGACTAGGCCCTAACACCAATATAGTCAAACGAGGGATGAAAAGAGTTTGACCAGG
* *
8768 CCCTAACACCAATACAGTCAAACGAGGGATG
66 CCCTAACACCAATACAGTCAAAAGAAGGATG
* ***
8799 AAAAGAGTTTGACTAGGCCCTAACACCAATATAGTCAAACGAGGGAAGATTTGAGTTTGACCAGG
1 AAAAGAGTTTGACTAGGCCCTAACACCAATATAGTCAAACGAGGGATGAAAAGAGTTTGACCAGG
* *
8864 CCCTGACACCAATACAGTCAAAAGAAGGAAG
66 CCCTAACACCAATACAGTCAAAAGAAGGATG
*** * * * * *
8895 ATTTGAGTTTTACTAGGCCCTAATACCAATATAGTCAAACAAGGGATGAAAAGAGTTTAACCAAG
1 AAAAGAGTTTGACTAGGCCCTAACACCAATATAGTCAAACGAGGGATGAAAAGAGTTTGACCAGG
* * *
8960 CCTTAACACCGATACAGTCAAATGAAGGATG
66 CCCTAACACCAATACAGTCAAAAGAAGGATG
*
8991 AAAATAGTTT
1 AAAAGAGTTT
9001 AACCGAGTAG
Statistics
Matches: 167, Mismatches: 34, Indels: 1
0.83 0.17 0.00
Matches are distributed among these distances:
95 19 0.11
96 148 0.89
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (96 bp):
AAAAGAGTTTGACTAGGCCCTAACACCAATATAGTCAAACGAGGGATGAAAAGAGTTTGACCAGG
CCCTAACACCAATACAGTCAAAAGAAGGATG
Found at i:11438 original size:13 final size:13
Alignment explanation
Indices: 11417--11446 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11407 ATCTAAAATT
*
11417 TTTTTTTCTTTTC
1 TTTTCTTCTTTTC
11430 TTTTCTTCTTTTC
1 TTTTCTTCTTTTC
11443 TTTT
1 TTTT
11447 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTCTTTTC
Found at i:16672 original size:11 final size:11
Alignment explanation
Indices: 16658--16682 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16648 AAGAAATGTC
16658 TAAAATGTTTT
1 TAAAATGTTTT
16669 TAAAATGTTTT
1 TAAAATGTTTT
16680 TAA
1 TAA
16683 GGTTTATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (11 bp):
TAAAATGTTTT
Found at i:17172 original size:161 final size:154
Alignment explanation
Indices: 16850--17279 Score: 434
Period size: 156 Copynumber: 2.7 Consensus size: 154
16840 TACCTGATAC
* ** * * * *
16850 CCCTAAAGGACTTGAAAATGATTTTAAAAGGGATGAACCTA-CCTAAATATCTATCTTTGGCATA
1 CCCTAAAGGACTT-AAAAAGATTAGAGATGGGATGAACCTATCCTAAATACCTATCTTCGGCATA
** ** * * * *
16914 AAGTAGACCTAGTGACAACCTAAGACTTGGTTTTAAAAAATTATCAAAATGCCCTTAGGGGACAC
65 AAGCGGACCCGGTGACAACCTAAGACTTAGTTCTAAAAAATTATCAAAATACCCTTAAGGGACAC
*
16979 CTTCGACCTGAAAGTATCCCAGTAA
130 CTTCGACCTGAAAGTATCCCAATAA
*
17004 CCCTAAAGGATTTAAAAAAGATATAGTTAAGATGGGATGAACCTATCCTAAATACCTATCTTCGG
1 CCCTAAAGGACTT-AAAAAGAT-TAG---AGATGGGATGAACCTATCCTAAATACCTATCTTCGG
*
17069 CATAGAAGCGGACCCGGTGGCAACCTAAGACTTAGTTCTAAAAAATTA-CAAAAATACCCTTATA
61 CATA-AAGCGGACCCGGTGACAACCTAAGACTTAGTTCTAAAAAATTATC-AAAATACCCTTA-A
* * * *
17133 GGTATACCTTCGACGTGAAAGTATCCTAATAA
123 GGGACACCTTCGACCTGAAAGTATCCCAATAA
* * * * * *
17165 CCCTAAAGGACTTAAAAATATTAGAGATAGGATCAACCTATCCTAAATGCCCACCTTCGGCATAA
1 CCCTAAAGGACTTAAAAAGATTAGAGATGGGATGAACCTATCCTAAATACCTATCTTCGGCAT-A
* * * * * *
17230 AAGCGGACTCGGTGACGACCT-AGAAGTTGGTTCTGAAAAATTATGAAAAT
65 AAGCGGACCCGGTGACAACCTAAG-ACTTAGTTCTAAAAAATTATCAAAAT
17280 GGCCATAAGA
Statistics
Matches: 228, Mismatches: 37, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
154 19 0.08
155 3 0.01
156 73 0.32
157 1 0.00
158 14 0.06
159 25 0.11
160 54 0.24
161 39 0.17
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (154 bp):
CCCTAAAGGACTTAAAAAGATTAGAGATGGGATGAACCTATCCTAAATACCTATCTTCGGCATAA
AGCGGACCCGGTGACAACCTAAGACTTAGTTCTAAAAAATTATCAAAATACCCTTAAGGGACACC
TTCGACCTGAAAGTATCCCAATAA
Found at i:20958 original size:13 final size:13
Alignment explanation
Indices: 20940--20967 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20930 TACAAAAGAT
20940 CAATGTATCGATA
1 CAATGTATCGATA
20953 CAATGTATCGATA
1 CAATGTATCGATA
20966 CA
1 CA
20968 TTGAGTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:21045 original size:19 final size:19
Alignment explanation
Indices: 21021--21123 Score: 92
Period size: 19 Copynumber: 5.6 Consensus size: 19
21011 CGATACATTA
21021 TATCGATACAAAACTTATG
1 TATCGATACAAAACTTATG
21040 TATCGATAC---A---ATG
1 TATCGATACAAAACTTATG
* *
21053 TATCAATACAACACTTATG
1 TATCGATACAAAACTTATG
*
21072 TATCGATACAACACTTATG
1 TATCGATACAAAACTTATG
** *
21091 TATCGATACAGTTACTGTTTG
1 TATCGATACA-AAACT-TATG
21112 TATCGATACAAA
1 TATCGATACAAA
21124 TTGTTTGAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
13 11 0.16
16 2 0.03
19 40 0.58
20 3 0.04
21 13 0.19
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (19 bp):
TATCGATACAAAACTTATG
Found at i:21062 original size:32 final size:32
Alignment explanation
Indices: 21006--21082 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
20996 GCAGTAGCTT
* * *
21006 TGTAGCGATACATTATATCGATACAAAACTTA
1 TGTATCGATACAATATATCAATACAAAACTTA
* *
21038 TGTATCGATACAATGTATCAATACAACACTTA
1 TGTATCGATACAATATATCAATACAAAACTTA
21070 TGTATCGATACAA
1 TGTATCGATACAA
21083 CACTTATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAATATATCAATACAAAACTTA
Found at i:26259 original size:33 final size:33
Alignment explanation
Indices: 26217--26284 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
26207 AAAACCCCAA
*
26217 AATCTAGGTTCAAAAAGACAACCGAATTATGCT
1 AATCTAGGTTCAAAAAAACAACCGAATTATGCT
* *
26250 AATCTAGGTTCAAAAAAATAACTGAATTATGCT
1 AATCTAGGTTCAAAAAAACAACCGAATTATGCT
26283 AA
1 AA
26285 CTTAGTGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (33 bp):
AATCTAGGTTCAAAAAAACAACCGAATTATGCT
Found at i:28648 original size:34 final size:34
Alignment explanation
Indices: 28609--28743 Score: 216
Period size: 34 Copynumber: 4.0 Consensus size: 34
28599 AAATATCTTA
* * * *
28609 CTCACCTAACACATTACCTAACACACCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
*
28643 TTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
28677 CTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
*
28711 CTCACCAAATACATCACCTAACATACCTAACAT
1 CTCACCAAATACATCACCTAACACACCTAACAT
28744 GCTTCACCTA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 94 1.00
ACGTcount: A:0.41, C:0.36, G:0.00, T:0.23
Consensus pattern (34 bp):
CTCACCAAATACATCACCTAACACACCTAACATT
Found at i:28740 original size:9 final size:10
Alignment explanation
Indices: 28653--28743 Score: 53
Period size: 9 Copynumber: 8.4 Consensus size: 10
28643 TTCACCAAAT
28653 ACATCACCTA
1 ACATCACCTA
28663 ACA-CACCTA
1 ACATCACCTA
*
28672 ACATTCTCACCAAA
1 ACA---TCACC-TA
28686 TACATCACCTA
1 -ACATCACCTA
28697 ACA-CACCTA
1 ACATCACCTA
*
28706 ACATTCTCACCAAA
1 ACA---TCACC-TA
28720 TACATCACCTA
1 -ACATCACCTA
28731 ACAT-ACCTA
1 ACATCACCTA
28740 ACAT
1 ACAT
28744 GCTTCACCTA
Statistics
Matches: 65, Mismatches: 4, Indels: 25
0.69 0.04 0.27
Matches are distributed among these distances:
9 27 0.42
10 10 0.15
11 2 0.03
12 10 0.15
13 8 0.12
14 2 0.03
15 6 0.09
ACGTcount: A:0.42, C:0.37, G:0.00, T:0.21
Consensus pattern (10 bp):
ACATCACCTA
Found at i:33506 original size:34 final size:34
Alignment explanation
Indices: 33467--33557 Score: 119
Period size: 34 Copynumber: 2.7 Consensus size: 34
33457 AAATATCTTA
* * * *
33467 CTCACCTAACACATTACCTAACACACCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
* * *
33501 TTCACCAAATAAATCACTTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAACATT
33535 CTCACCAAATACATCACCTAACA
1 CTCACCAAATACATCACCTAACA
33558 TGCTTCACCT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.42, C:0.34, G:0.00, T:0.24
Consensus pattern (34 bp):
CTCACCAAATACATCACCTAACACACCTAACATT
Found at i:37669 original size:3 final size:3
Alignment explanation
Indices: 37661--37698 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
37651 ATCACAAATA
37661 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
37699 AGGCAACATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:38006 original size:15 final size:15
Alignment explanation
Indices: 37988--38021 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
37978 AAAAAAAATT
37988 AAAAATTTGAATTTA
1 AAAAATTTGAATTTA
38003 AAAAATTTGAATTTA
1 AAAAATTTGAATTTA
38018 AAAA
1 AAAA
38022 GTTTAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
AAAAATTTGAATTTA
Found at i:38649 original size:16 final size:17
Alignment explanation
Indices: 38623--38656 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
38613 TCTTTTAAAT
*
38623 AAAAATATAAAGATTAA
1 AAAAATATAAAAATTAA
38640 AAAAAT-TAAAAATTAA
1 AAAAATATAAAAATTAA
38656 A
1 A
38657 TTAAACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAATATAAAAATTAA
Found at i:39477 original size:5 final size:5
Alignment explanation
Indices: 39459--39497 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
39449 GTAATCTTAA
* *
39459 AAAAT ATAAT AAAAC AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
39498 ATTTGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:40204 original size:15 final size:16
Alignment explanation
Indices: 40180--40221 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
40170 TAAGATAATC
*
40180 TGAACACAAAAA-ACT
1 TGAACTCAAAAATACT
*
40195 TGAATTCAAAAATACT
1 TGAACTCAAAAATACT
40211 TGAACTCAAAA
1 TGAACTCAAAA
40222 TGATCTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (16 bp):
TGAACTCAAAAATACT
Found at i:40275 original size:17 final size:16
Alignment explanation
Indices: 40216--40275 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
40206 ATACTTGAAC
*
40216 TCAAAATGATCTAAAT
1 TCAAAATAATCTAAAT
40232 TCAAAATATATCTAAAT
1 TCAAAATA-ATCTAAAT
* *
40249 TAAAAAATAATTTAAAT
1 T-CAAAATAATCTAAAT
40266 TCAAATATAA
1 TCAAA-ATAA
40276 CCTGATCTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.27
17 21 0.57
18 6 0.16
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (16 bp):
TCAAAATAATCTAAAT
Found at i:43933 original size:52 final size:52
Alignment explanation
Indices: 43788--43913 Score: 225
Period size: 52 Copynumber: 2.4 Consensus size: 52
43778 AATATGAAAC
*
43788 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGTAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGCAAA
* *
43840 TTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGCAAA
43892 TTTGCCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
43914 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGCAAA
Found at i:43940 original size:13 final size:13
Alignment explanation
Indices: 43922--43946 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43912 CAAAGATCAG
43922 TGTATCGATACAA
1 TGTATCGATACAA
43935 TGTATCGATACA
1 TGTATCGATACA
43947 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:44009 original size:13 final size:13
Alignment explanation
Indices: 43991--44074 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
43981 AGCTTCGTAG
43991 CGATACATTGTAT
1 CGATACATTGTAT
44004 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
44023 CGATACATTGTAT
1 CGATACATTGTAT
44036 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
44055 CGATACATTGTAT
1 CGATACATTGTAT
44068 CGATACA
1 CGATACA
44075 ACACTTATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:44023 original size:19 final size:18
Alignment explanation
Indices: 43999--44094 Score: 95
Period size: 19 Copynumber: 5.7 Consensus size: 18
43989 AGCGATACAT
43999 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
44018 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
44031 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
44050 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
44063 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
44082 TGTATCGATACAA
1 TGTATCGATACAA
44095 TTTCTGTTTG
Statistics
Matches: 65, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
16 4 0.06
18 2 0.03
19 35 0.54
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:44032 original size:32 final size:32
Alignment explanation
Indices: 43991--44093 Score: 197
Period size: 32 Copynumber: 3.2 Consensus size: 32
43981 AGCTTCGTAG
*
43991 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
44023 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
44055 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
44087 CGATACA
1 CGATACA
44094 ATTTCTGTTT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:44911 original size:13 final size:13
Alignment explanation
Indices: 44893--44917 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44883 TACTATGAAC
44893 ATGTATCGATACA
1 ATGTATCGATACA
44906 ATGTATCGATAC
1 ATGTATCGATAC
44918 TAAGCAATAT
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):
ATGTATCGATACA
Found at i:44935 original size:33 final size:32
Alignment explanation
Indices: 44875--44938 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
44865 CTTTTTAAGG
*
44875 TGTATCAATACTATGAACATGTATCGATACAA
1 TGTATCAATACTAAGAACATGTATCGATACAA
* *
44907 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCAATACTAAG-AACATGTATCGATACA
44939 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (32 bp):
TGTATCAATACTAAGAACATGTATCGATACAA
Found at i:45654 original size:21 final size:23
Alignment explanation
Indices: 45616--45659 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
45606 CTCTTTTTGT
45616 TATCTCTCCCAATATTTA-CAAAA
1 TATCTCTCCC-ATATTTATCAAAA
*
45639 TATCTCTCCC-TTTTTATCAAA
1 TATCTCTCCCATATTTATCAAA
45660 TTTATTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 4 0.21
23 10 0.53
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (23 bp):
TATCTCTCCCATATTTATCAAAA
Found at i:47514 original size:13 final size:13
Alignment explanation
Indices: 47496--47533 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
47486 TTTCTAGATA
47496 TATCGATACATTG
1 TATCGATACATTG
*
47509 TATCGATACAATG
1 TATCGATACATTG
47522 TATCGATACATT
1 TATCGATACATT
47534 CTGGGAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:52584 original size:19 final size:18
Alignment explanation
Indices: 52559--52626 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
52549 AATTCAACAA
52559 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
52577 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
52593 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
52609 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
52627 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 1 0.02
19 27 0.63
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:52598 original size:13 final size:13
Alignment explanation
Indices: 52580--52604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52570 ACATAAGTGT
52580 TGTATCGATACAA
1 TGTATCGATACAA
52593 TGTATCGATACA
1 TGTATCGATACA
52605 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:52598 original size:32 final size:32
Alignment explanation
Indices: 52561--52623 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
52551 TTCAACAATT
*
52561 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
52593 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
52624 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:52684 original size:13 final size:13
Alignment explanation
Indices: 52666--52691 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52656 CATTTTTCTA
52666 TGTATCGATACAT
1 TGTATCGATACAT
52679 TGTATCGATACAT
1 TGTATCGATACAT
52692 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:52688 original size:33 final size:33
Alignment explanation
Indices: 52646--52712 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
52636 GCCAAGGAAA
***
52646 TGTATCGATACATTTTTCTATGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
*
52679 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
52712 T
1 T
52713 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTATGTATCGATACAT
Found at i:55124 original size:51 final size:51
Alignment explanation
Indices: 55064--55180 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 51
55054 AATTCTCCAC
55064 AATCGGGGATA-TCCCAACTCCGATTTCATTT-TCAAAACA-CTAATTTTCTAT
1 AATCGGGGATACT-CCAACTCCGATTTCATTTCT-AAAACATC-AATTTTCTAT
* *
55115 AATCGGGGATACTCCAACTCTGATTTTATTTCTAAAACATCAA-TTT-T-T
1 AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTAT
*
55163 CATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
55181 CCCGTTAATC
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
48 18 0.30
49 1 0.02
50 3 0.05
51 35 0.58
52 3 0.05
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTAT
Found at i:55234 original size:28 final size:27
Alignment explanation
Indices: 55162--55237 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
55152 CATCAATTTT
55162 TCATCGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
55189 TCATCGGGGATACTCCAACCCCGTT-A
1 TCATCGGGGATACTCCAACCCCGTTAA
**
55215 TTTTCGAGGGGATACTCCAACCC
1 TCATC--GGGGATACTCCAACCC
55238 TCGGCTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 4 0.09
27 25 0.56
28 16 0.36
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.24
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:55336 original size:80 final size:80
Alignment explanation
Indices: 55191--55397 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
55181 CCCGTTAATC
* * *
55191 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTCGGCTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTCGACTTTATTTCAAAAA
** *
55256 TA-TTAATTTCTCATA
66 TACCAAATTT-TCACA
* * * *
55271 ATCGGGGATACTCTAACCCCGTTATCTCCGAGGGGATACTCCAACTC-CGATTTTATTTCCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTCGACTTTATTT-CAAAA
55335 ATACCAAATTTTCACA
65 ATACCAAATTTTCACA
* * ***
55351 ATTGGGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCC
55398 CGTTACCTCC
Statistics
Matches: 107, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
79 9 0.08
80 93 0.87
81 5 0.05
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTCGACTTTATTTCAAAAA
TACCAAATTTTCACA
Found at i:55387 original size:108 final size:107
Alignment explanation
Indices: 55271--55481 Score: 300
Period size: 108 Copynumber: 2.0 Consensus size: 107
55261 ATTTCTCATA
* * *
55271 ATCGGGGATACTCTAACCCCGTTATCTCCGAGGGGATACTCCAACTCC-GATTTTATTTCCAAAA
1 ATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAG-TTTTA-TTCCAAAA
*
55335 ATACCAAATTT-TCACAATTGGGGATACTCCAACCTCGTTATTTC
64 ATA-CAAATTTCTCACAATTGGGGATACTCCAACCCCGTTATTTC
*
55379 ATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGTTTTATTCCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGTTTTATTCCAAAAAT
** * *
55444 ACTGATTTCTCATAATTGGGGATGCTCCAACCCCGTTA
66 ACAAATTTCTCACAATTGGGGATACTCCAACCCCGTTA
55482 CCTCCGAGGG
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
106 5 0.05
107 36 0.39
108 50 0.54
109 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (107 bp):
ATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGTTTTATTCCAAAAAT
ACAAATTTCTCACAATTGGGGATACTCCAACCCCGTTATTTC
Found at i:55413 original size:28 final size:28
Alignment explanation
Indices: 55354--55426 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
55344 TTTCACAATT
* ** **
55354 GGGGATACTCCAACCTCGTTATTTCATC
1 GGGGATACTCCAACCCCGTTACCTCAGA
*
55382 GGGGATACTCCAACCCCGTTACCTCCGA
1 GGGGATACTCCAACCCCGTTACCTCAGA
55410 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
55427 AGTTTTATTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.22
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTACCTCAGA
Found at i:55490 original size:187 final size:186
Alignment explanation
Indices: 55119--55588 Score: 585
Period size: 187 Copynumber: 2.5 Consensus size: 186
55109 TTCTATAATC
* * *
55119 GGGGATACTCCAACTCTGATTTTATTTCTAAAACAT-CAATTTT-TC-ATCGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAA-ATACAATTTTCACAATCGGGGATACTCCAAC
* ** * *
55181 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTCGGCTT
65 CCCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCTCAGCTT
* * * * *
55245 TATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCTAACCCCGTTATCTCCGA
130 TATTCCCAAAATACTAATTTCTCATAATCGGGGATACTCCAACCCCGTTACCTCCGA
*
55302 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAATTTTCACAATTGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATA-C-AATTTTCACAATCGGGGATACTCCAA
* *
55367 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCC-CAGTT
64 CCCCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCTCAGCT
* * *
55431 TTATTCCCAAAATACTGATTTCTCATAATTGGGGATGCTCCAACCCCGTTACCTCCGA
129 TTATTCCCAAAATACTAATTTCTCATAATCGGGGATACTCCAACCCCGTTACCTCCGA
* * * ** * *
55489 GGGGATACTCCAATTTCTATTTTATTTCCTAATCAT-CGATTTTTCACAACCGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCC-AAAAATAC-AATTTTCACAATCGGGGATACTCCAA
* *
55553 CCCCGTTATTTTCA-AGGGGATACTCCAACCTCGTTA
64 CCCCGTTA-TTTCATCGGGGATACTCCAACCCCGTTA
55589 TTATCTTCAA
Statistics
Matches: 248, Mismatches: 31, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
182 2 0.01
183 31 0.12
184 1 0.00
185 6 0.02
186 52 0.21
187 106 0.43
188 50 0.20
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.31
Consensus pattern (186 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACAATTTTCACAATCGGGGATACTCCAACC
CCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCTCAGCTTT
ATTCCCAAAATACTAATTTCTCATAATCGGGGATACTCCAACCCCGTTACCTCCGA
Found at i:55501 original size:107 final size:108
Alignment explanation
Indices: 55274--55501 Score: 291
Period size: 107 Copynumber: 2.1 Consensus size: 108
55264 TCTCATAATC
* * *
55274 GGGGATACTCTAACCCCGTTATCTCCGAGGGGATACTCCAACTCCGATTTTATTTCCAAAAATAC
1 GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAAATAC
* ** **
55339 CAAATTTTCACAATTGGGGATACTCCAACCTCGTTATTTCATC
66 CAAATTTTCACAATTGGGGATACTCCAACCCCGTTACCTCAGA
*
55382 GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCC-AGTTTTA-TTCCCAAAATA
1 GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGA-TTTTATTTCCAAAAATA
** * * *
55445 -CTGATTTCTCATAATTGGGGATGCTCCAACCCCGTTACCTCCGA
65 CCAAATTT-TCACAATTGGGGATACTCCAACCCCGTTACCTCAGA
55489 GGGGATACTCCAA
1 GGGGATACTCCAA
55502 TTTCTATTTT
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
106 5 0.05
107 52 0.50
108 47 0.45
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.27
Consensus pattern (108 bp):
GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAAATAC
CAAATTTTCACAATTGGGGATACTCCAACCCCGTTACCTCAGA
Found at i:55513 original size:79 final size:79
Alignment explanation
Indices: 55381--55582 Score: 230
Period size: 79 Copynumber: 2.6 Consensus size: 79
55371 GTTATTTCAT
55381 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGTTTTATTCCCAAA--AT
1 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGTTTTATTCCCAAATCAT
* *
55444 ACTGATTTCTCATAAT
66 -C-GATTTCTCACAAC
* * ** * * *
55460 TGGGGATGCTCCAACCCCGTTACCTCCGAGGGGATACTCCAATTTCTA-TTTTATTTCCTAATCA
1 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAA-CCCCAGTTTTATTCCCAAATCA
*
55524 TCGATTTTTCACAAC
65 TCGATTTCTCACAAC
** * *
55539 CGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACC
1 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACC
55583 TCGTTATTAT
Statistics
Matches: 102, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
79 97 0.95
80 3 0.03
81 2 0.02
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGTTTTATTCCCAAATCAT
CGATTTCTCACAAC
Found at i:61790 original size:60 final size:58
Alignment explanation
Indices: 61684--62386 Score: 760
Period size: 55 Copynumber: 12.3 Consensus size: 58
61674 GCCCTTCCAC
* *
61684 TCCTCAAAGAGCAGTACGCCTTTTTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAG
1 TCCTCAAAGAGCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAG
*
61743 TCCTCAAAAAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAG
1 TCCTCAAAGAGCAGGACGCC-TTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAG
**
61803 TCCTCAAAGAGCAGGACG-C---CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAG
1 TCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-TAG
* * *
61858 TCCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAG
1 TCCTCAAAGAGCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAG
* * **
61917 TCCTCAAAGAGTAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAG
1 TCCTCAAAGAGCAGGACGCCTT-T-CTTTTAAAGCCCACACAAGTTGGTGGCACCTT-TAG
* * * *
61978 TCCTTAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCAG
1 TCCTCAAAGAGCAGGACGC-CTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT-AG
* * *
62038 TCCCCAAAGAGCAGGACACCTTTC----AAAGCCCACACAAGTTGGTGGCA-TTTTCAG
1 TCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-AG
* * *
62092 TCCCCAAAGAGCAGGACACCTTTC----AAAGCCCACACAAGTTGGTGGCA-TTTTCCAG
1 TCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT--AG
* **
62147 TCCTCAAAGAGCAGGAC-AC---CTTTTAAAGCCCACACAAGTTGGTGGCACCTCCAG
1 TCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAG
* * *
62201 TCCTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAG
1 TCCTCAAAGAGCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT--AG
*
62261 TCCTCAAAGAGCAGGACACC--TC--TTAAAGCCCACACAAGTTGGTGGCACCTTTCAG
1 TCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-AG
* *
62316 TCCTCAAAGAGCAGGACACCTTTC----AAAGCCCACACGAGTTGGTGGCACCTTTTAG
1 TCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTTAG
62371 TCCTCAAAGAGCAGGA
1 TCCTCAAAGAGCAGGA
62387 TACACTTTAT
Statistics
Matches: 570, Mismatches: 44, Indels: 64
0.84 0.06 0.09
Matches are distributed among these distances:
51 1 0.00
54 130 0.23
55 152 0.27
56 8 0.01
57 4 0.01
58 3 0.01
59 76 0.13
60 152 0.27
61 42 0.07
62 2 0.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (58 bp):
TCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAG
Found at i:61889 original size:114 final size:114
Alignment explanation
Indices: 61709--62386 Score: 873
Period size: 114 Copynumber: 6.0 Consensus size: 114
61699 ACGCCTTTTT
** *
61709 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAAAGCAGGACGCCTTTTCCTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT-CTTTT
*
61773 AAAGCCCACACAAGTTGGTGGCACCTTT-AGTCCTCAAAGAGCAGGACGCC
65 AAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACACC
*
61823 TTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCCCAAAGAGCAGGACGCCTTTTCTTTTA
1 TTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTA
* * * *
61888 AAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAAGAGTAGGACGCCTTC
66 AAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGAC-AC--C
* * *
61940 TCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTTAAAGAGCAGGATGCTTTTTCTT
1 T--TTT-AAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTT
* *
62005 TTCAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCCCAAAGAGCAGGACACC
63 TT-AAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACACC
* * *
62058 TTTCAAAGCCCACACAAGTTGGTGGCATTTTC-AGTCCCCAAAGAGCAGGACACC-TTTC----A
1 TTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTA
*
62117 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC
66 AAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGGACACC
** * * *
62167 TTTTAAAGCCCACACAAGTTGGTGGCA-CCTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTCA
1 TTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTA
*
62231 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC
66 AAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGGACACC
* * *
62281 TCTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACACC-TTTC----
1 TTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT
* *
62340 AAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGA
65 AAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGA
62387 TACACTTTAT
Statistics
Matches: 506, Mismatches: 39, Indels: 42
0.86 0.07 0.07
Matches are distributed among these distances:
108 29 0.06
109 67 0.13
110 44 0.09
111 3 0.01
113 7 0.01
114 172 0.34
115 74 0.15
116 4 0.01
117 2 0.00
118 2 0.00
119 3 0.01
120 57 0.11
121 42 0.08
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (114 bp):
TTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTA
AAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACACC
Found at i:62035 original size:28 final size:28
Alignment explanation
Indices: 62003--62143 Score: 86
Period size: 28 Copynumber: 5.2 Consensus size: 28
61993 ATGCTTTTTC
62003 TTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAAAGCCCACACAAGTTGGTGGCA
* **
62031 TTTTC--AGTCCC-CA-AAG-AGCAGGACA
1 TTTTCAAAG-CCCACACAAGTTGGTGG-CA
*
62056 CCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAAAGCCCACACAAGTTGGTGGCA
* **
62085 TTTTC--AGTCCC-CA-AAG-AGCAGGACA
1 TTTTCAAAG-CCCACACAAGTTGGTGG-CA
*
62110 CCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAAAGCCCACACAAGTTGGTGGCA
62139 TTTTC
1 TTTTC
62144 CAGTCCTCAA
Statistics
Matches: 81, Mismatches: 16, Indels: 32
0.63 0.12 0.25
Matches are distributed among these distances:
24 6 0.07
25 10 0.12
26 16 0.20
27 12 0.15
28 21 0.26
29 10 0.12
30 6 0.07
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (28 bp):
TTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:62450 original size:42 final size:42
Alignment explanation
Indices: 62364--62458 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
62354 TTGGTGGCAC
* *
62364 CTTTTAGTCCTCAAAGAGCAGGATACACTTTATTTTCCTCTTT
1 CTTTTA-TCCTCAAAGAGCAGGACACACTTTATTTCCCTCTTT
* ** *
62407 CTTTTATCCTCAGAGAGCAGGACGTA-TTTCATTTCCCTTTTT
1 CTTTTATCCTCAAAGAGCAGGACACACTTT-ATTTCCCTCTTT
*
62449 CTTTTGTCCT
1 CTTTTATCCT
62459 TGGAAAATGG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 3 0.07
42 35 0.80
43 6 0.14
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (42 bp):
CTTTTATCCTCAAAGAGCAGGACACACTTTATTTCCCTCTTT
Found at i:63114 original size:21 final size:21
Alignment explanation
Indices: 63090--63147 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
63080 AAAATTTCCA
63090 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
* *
63111 AATGTATCGAAACATTTGTGG
1 AATGTATCGATACATTTGTAG
63132 AATGTATCGATACATT
1 AATGTATCGATACATT
63148 CTACAAATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:63156 original size:21 final size:20
Alignment explanation
Indices: 63083--63162 Score: 70
Period size: 21 Copynumber: 3.9 Consensus size: 20
63073 GAAAAAAAAA
*
63083 ATTTCCAAATGTATCGATAC
1 ATTTACAAATGTATCGATAC
** *
63103 ATTTGTAGAATGTATCGAAAC
1 ATTTACA-AATGTATCGATAC
***
63124 ATTTGTGGAATGTATCGATAC
1 ATTT-ACAAATGTATCGATAC
63145 ATTCTACAAATGTATCGA
1 ATT-TACAAATGTATCGA
63163 CACAAGGTCC
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
20 5 0.11
21 41 0.87
22 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
ATTTACAAATGTATCGATAC
Found at i:63227 original size:19 final size:18
Alignment explanation
Indices: 63202--63269 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
63192 AATTCAACAA
63202 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
63220 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
63236 --TGTATCAATACATAAG
1 TTTGTATCGATACATAAG
63252 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
63270 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
18 1 0.02
19 26 0.63
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:63241 original size:32 final size:32
Alignment explanation
Indices: 63204--63266 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
63194 TTCAACAATT
* *
63204 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAGTATTGTATCGATACAA
63236 TGTATCAATACATAAGTATTGTATCGATACA
1 TGTATCAATACATAAGTATTGTATCGATACA
63267 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCAATACATAAGTATTGTATCGATACAA
Found at i:63327 original size:13 final size:13
Alignment explanation
Indices: 63309--63334 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63299 CATTTTTTTG
63309 TGTATCGATACAT
1 TGTATCGATACAT
63322 TGTATCGATACAT
1 TGTATCGATACAT
63335 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:65801 original size:51 final size:48
Alignment explanation
Indices: 65705--65821 Score: 148
Period size: 51 Copynumber: 2.4 Consensus size: 48
65695 AATTCTCCGC
*
65705 AATCGGGGATA-TCCCAACTCCGATTTTATTTTCAAAACATTAATTTTCTAT
1 AATCGGGGATACT-CCAACTCCGATTTTATTTTCAAAACATCAA-TTT-T-T
*
65756 AATCGGGGATACTCCAACTCCGATTTTA-TTTCTAAAATATCAATTTTT
1 AATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACATCAATTTTT
*
65804 CATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
65822 CTCGTTAATC
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
48 18 0.30
49 1 0.02
50 7 0.11
51 34 0.56
52 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (48 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACATCAATTTTT
Found at i:65841 original size:27 final size:27
Alignment explanation
Indices: 65803--65879 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
65793 TATCAATTTT
*
65803 TCATCGGGGATACTCCAACCTCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
*
65830 TCATCGGGGATACTCCAACCCCGTTAT
1 TCATCGGGGATACTCCAACCCCGTTAA
** *
65857 TTTTGAGGGGATACTCCAACCCC
1 TCAT-CGGGGATACTCCAACCCC
65880 CGGCTTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 27 0.61
28 17 0.39
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.26
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:66000 original size:80 final size:79
Alignment explanation
Indices: 65837--66040 Score: 221
Period size: 80 Copynumber: 2.6 Consensus size: 79
65827 TAATCATCGG
** * * * **
65837 GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAATATTA
1 GGATACTCCAACCCCGTTATTTCAGAGGGGATACTCCAA-CCCCGACTTTATTTCAAAAACACAA
* *
65902 ATTTCTCATAATCGA
65 ATTTCTCACAATCAA
* * * *
65917 GGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCA
1 GGATACTCCAACCCCGTTATTTCAGAGGGGATACTCCAACCCCGACTTTATTT-CAAAAACA-CA
*
65982 AATTT-TCACAATTAA
64 AATTTCTCACAATCAA
* **
65997 GGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCG
1 GGATACTCCAACCCCGTTATTTCAGAGGGGATACTCCAACCCCG
66041 TTACCTCCGA
Statistics
Matches: 103, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
79 11 0.11
80 87 0.84
81 5 0.05
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (79 bp):
GGATACTCCAACCCCGTTATTTCAGAGGGGATACTCCAACCCCGACTTTATTTCAAAAACACAAA
TTTCTCACAATCAA
Found at i:66097 original size:187 final size:186
Alignment explanation
Indices: 65760--66229 Score: 599
Period size: 187 Copynumber: 2.5 Consensus size: 186
65750 TTCTATAATC
* * *
65760 GGGGATACTCCAACTCCGATTTTATTTCTAAAATATCAATTTT-TC-ATCGGGGATACTCCAACC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTCACAATCGGGGATACTCCAACC
* ** **
65823 TCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCCGGCTTT
66 TCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCCGGCTTT
* *
65887 ATTTCTAAAATATTAATTTCTCATAATCGAGGATACTCCAACCCCGTTATCTCCGA
131 ATTCCTAAAATATTAATTTCTCATAATCGAGGATACTCCAACCCCGTTACCTCCGA
* ***
65943 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTTCACAATTAAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCC-AAAACATC-AATTTTCACAATCGGGGATACTCCAA
* *
66008 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCTAA-CCCCGGTT
64 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCCGGCT
* * * *
66072 TTATTCCTAAAATATTGATTTCTCATAATTGGGGATACTCCAACTCCGTTACCTCCGA
129 TTATTCCTAAAATATTAATTTCTCATAATCGAGGATACTCCAACCCCGTTACCTCCGA
* * * * * *
66130 GGGGATACTCCAATTTCGATTTTATTTCCTAATCATCGATTTTTCACAACCGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAACATC-AATTTTCACAATCGGGGATACTCCAAC
* * * *
66195 CCCGTTATTTTCA-AGGGGATACTCTAACCTCGTTA
65 CTCGTTA-TTTCATCGGGGATACTCCAACCCCGTTA
66230 TTATCTCCAA
Statistics
Matches: 246, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
183 28 0.11
184 6 0.02
185 6 0.02
186 53 0.22
187 112 0.46
188 41 0.17
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (186 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTCACAATCGGGGATACTCCAACC
TCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCCGGCTTT
ATTCCTAAAATATTAATTTCTCATAATCGAGGATACTCCAACCCCGTTACCTCCGA
Found at i:66115 original size:79 final size:79
Alignment explanation
Indices: 66022--66256 Score: 253
Period size: 79 Copynumber: 3.0 Consensus size: 79
66012 GTTATTTCAT
*
66022 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCTAACCCCGGTTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCTAACCTCGGTTTTATTCCTAAAATAT
*
66087 TGATTTCTCATAAT
66 TGATTTCTCATAAC
* * * ** *
66101 TGGGGATACTCCAACTCCGTTACCTCCGAGGGGATACTCCAATTTCGATTTTATTTCCT--AATC
1 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCTAACCTCGGTTTTA-TTCCTAAAAT-
* * *
66164 ATCGATTTTTCACAAC
64 ATTGATTTCTCATAAC
** * *
66180 CGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCTAACCTC-GTTATTATCTCC-AAAAT
1 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCTAACCTCGGTT-TTAT-TCCTAAAAT
*
66243 ATTAAATTTCTCAT
64 ATT-GATTTCTCAT
66257 CGGGACATAT
Statistics
Matches: 124, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
78 6 0.05
79 103 0.83
80 15 0.12
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCTAACCTCGGTTTTATTCCTAAAATAT
TGATTTCTCATAAC
Found at i:68292 original size:16 final size:16
Alignment explanation
Indices: 68263--68306 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
68253 AACTTAGGAT
*
68263 TTTCTTTTTATTTATT-
1 TTTCTTATT-TTTATTC
68279 TTTGCTTATTTTTATTC
1 TTT-CTTATTTTTATTC
68296 TTTCTTATTTT
1 TTTCTTATTTT
68307 AGTTCACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTCTTATTTTTATTC
Found at i:71660 original size:25 final size:26
Alignment explanation
Indices: 71632--71686 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
71622 TAAAATGCAA
*
71632 AATTTGAAAAATTTTC-TTTCAAGGC
1 AATTTGAAAAATTTTCATTTAAAGGC
*
71657 AATTT-TAAAATTTTCATTTAAAGGC
1 AATTTGAAAAATTTTCATTTAAAGGC
71682 -ATTTG
1 AATTTG
71687 GAGTCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (26 bp):
AATTTGAAAAATTTTCATTTAAAGGC
Found at i:74506 original size:13 final size:13
Alignment explanation
Indices: 74488--74512 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74478 CCTTTTACTA
74488 TGTATCGATACAT
1 TGTATCGATACAT
74501 TGTATCGATACA
1 TGTATCGATACA
74513 ATGTCTCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:74587 original size:20 final size:20
Alignment explanation
Indices: 74561--74615 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
74551 CTACCAGTTT
74561 CATGTATCGATACAATTAAG
1 CATGTATCGATACAATTAAG
* *
74581 TATGTATCGATACAA-TCAG
1 CATGTATCGATACAATTAAG
74600 CATGTATCGATACAAT
1 CATGTATCGATACAAT
74616 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTAAG
Found at i:74619 original size:13 final size:13
Alignment explanation
Indices: 74601--74627 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
74591 TACAATCAGC
74601 ATGTATCGATACA
1 ATGTATCGATACA
74614 ATGTATCGATACA
1 ATGTATCGATACA
74627 A
1 A
74628 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:74643 original size:33 final size:32
Alignment explanation
Indices: 74582--74646 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
74572 ACAATTAAGT
* *
74582 ATGTATCGATACAATCAGCATGTATCGATACA
1 ATGTATCGATACAAGCAGAATGTATCGATACA
*
74614 ATGTATCGATACAAAGCATAATGTATCGATACA
1 ATGTATCGATAC-AAGCAGAATGTATCGATACA
74647 TCTGGATGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAGCAGAATGTATCGATACA
Found at i:81493 original size:21 final size:21
Alignment explanation
Indices: 81469--81519 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
81459 GATTTGTAAC
* *
81469 TTCTTCTTTGTCTTATTTAAA
1 TTCTTCTTCGGCTTATTTAAA
81490 TTCTTCTTCGGCTTATTTAAA
1 TTCTTCTTCGGCTTATTTAAA
81511 TTCTTCTTC
1 TTCTTCTTC
81520 TTCAATGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.20, G:0.06, T:0.59
Consensus pattern (21 bp):
TTCTTCTTCGGCTTATTTAAA
Found at i:83350 original size:43 final size:43
Alignment explanation
Indices: 83284--83380 Score: 185
Period size: 43 Copynumber: 2.3 Consensus size: 43
83274 TTTCATAATA
83284 TATCGATACATGCATTTGAAATTTATAGCCGTTGGACACATTG
1 TATCGATACATGCATTTGAAATTTATAGCCGTTGGACACATTG
*
83327 TATCAATACATGCATTTGAAATTTATAGCCGTTGGACACATTG
1 TATCGATACATGCATTTGAAATTTATAGCCGTTGGACACATTG
83370 TATCGATACAT
1 TATCGATACAT
83381 TTTACTATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (43 bp):
TATCGATACATGCATTTGAAATTTATAGCCGTTGGACACATTG
Found at i:83406 original size:13 final size:13
Alignment explanation
Indices: 83388--83412 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83378 CATTTTACTA
83388 TGTATCGATACAT
1 TGTATCGATACAT
83401 TGTATCGATACA
1 TGTATCGATACA
83413 ATGTCCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:83424 original size:33 final size:33
Alignment explanation
Indices: 83364--83434 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
83354 GCCGTTGGAC
* * *
83364 ACATTGTATCGATACATTTTACTATGTATCGAT
1 ACATTGTATCGATACAATGTACCATGTATCGAT
* *
83397 ACATTGTATCGATACAATGTCCCATGTATTGAT
1 ACATTGTATCGATACAATGTACCATGTATCGAT
83430 ACATT
1 ACATT
83435 TCACTTAGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (33 bp):
ACATTGTATCGATACAATGTACCATGTATCGAT
Found at i:83504 original size:19 final size:20
Alignment explanation
Indices: 83461--83514 Score: 92
Period size: 19 Copynumber: 2.8 Consensus size: 20
83451 CTGTCAGTTT
83461 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
*
83481 TATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
83500 CATGTATCGATACAA
1 CATGTATCGATACAA
83515 AGCATAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:83526 original size:20 final size:19
Alignment explanation
Indices: 83462--83533 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
83452 TGTCAGTTTC
* *
83462 ATGTATCGATACAATTGAGT
1 ATGTATCGATACAA-AGAGA
* *
83482 ATGTATCGATACAATGAGC
1 ATGTATCGATACAAAGAGA
*
83501 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAG-AGA
*
83521 ATGTATCAATACA
1 ATGTATCGATACA
83534 GTTGGATGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 19 0.41
20 27 0.59
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (19 bp):
ATGTATCGATACAAAGAGA
Found at i:88206 original size:2 final size:2
Alignment explanation
Indices: 88199--88231 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
88189 AGTCAAGCAC
88199 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 A
88232 AACTAATGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88542 original size:134 final size:135
Alignment explanation
Indices: 88300--88568 Score: 414
Period size: 134 Copynumber: 2.0 Consensus size: 135
88290 ATATTGATAA
*
88300 TTGACTCTATATTTAATACTTATATTCATTATATATTTAAATATGAATATAAAAAAAATTAACAA
1 TTGACTCTATATTTAATACGTATATTCATTATATATTTAAATATGAATATAAAAAAAATTAACAA
* * * *
88365 AAATTGAACCTAATTATATACAATACTCACTTTGAATCTGATTAATTATAAAATTAAGATTCGTT
66 AAATTAAACATAATTATATACAATACTCACTTTGAATATGATTAATTATAAAATTAAGATTCGCT
88430 AAGTT
131 AAGTT
* * * *
88435 TTGACTTTATGTTTAATACGTATGTTCATTATATATTTGAATATGAATAT-AAAAAAATTAACAA
1 TTGACTCTATATTTAATACGTATATTCATTATATATTTAAATATGAATATAAAAAAAATTAACAA
* * * *
88499 AAATTAAACATAATTGTATTCAATATTCACTTTGAATATGATTAATTATAAAATTAAGATTTGCT
66 AAATTAAACATAATTATATACAATACTCACTTTGAATATGATTAATTATAAAATTAAGATTCGCT
88564 AAGTT
131 AAGTT
88569 CGTAAATAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
134 76 0.63
135 45 0.37
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.41
Consensus pattern (135 bp):
TTGACTCTATATTTAATACGTATATTCATTATATATTTAAATATGAATATAAAAAAAATTAACAA
AAATTAAACATAATTATATACAATACTCACTTTGAATATGATTAATTATAAAATTAAGATTCGCT
AAGTT
Found at i:93065 original size:2 final size:2
Alignment explanation
Indices: 93058--93085 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
93048 TATACGTTTA
93058 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
93086 TGATTTTAGA
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:95496 original size:15 final size:16
Alignment explanation
Indices: 95471--95500 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
95461 ATATAATAAA
95471 TTATAATTTTTTTACC
1 TTATAATTTTTTTACC
95487 TTAT-ATTTTTTTAC
1 TTATAATTTTTTTAC
95501 TTGACTTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATAATTTTTTTACC
Found at i:95702 original size:19 final size:18
Alignment explanation
Indices: 95674--95709 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
95664 AATTTATTTA
95674 TTTATTTATTTATTTTTG
1 TTTATTTATTTATTTTTG
*
95692 TTTATTTTATTTGTTTTT
1 TTTA-TTTATTTATTTTT
95710 TTTTCTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.81
Consensus pattern (18 bp):
TTTATTTATTTATTTTTG
Found at i:95703 original size:23 final size:22
Alignment explanation
Indices: 95670--95713 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
95660 AAACAATTTA
95670 TTTATTTATTTATTTATTTTTG
1 TTTATTTATTTATTTATTTTTG
* *
95692 TTTATTTTATTTGTTTTTTTTT
1 TTTA-TTTATTTATTTATTTTT
95714 CTAAGATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.82
Consensus pattern (22 bp):
TTTATTTATTTATTTATTTTTG
Found at i:96223 original size:18 final size:16
Alignment explanation
Indices: 96199--96244 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
96189 TTATTATACA
96199 TATAATAAATATATATG
1 TATAATAAATATATA-G
*
96216 TAATAATAAACATATAG
1 T-ATAATAAATATATAG
*
96233 TATAATACATAT
1 TATAATAAATAT
96245 CCATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 9 0.36
17 3 0.12
18 13 0.52
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (16 bp):
TATAATAAATATATAG
Found at i:97895 original size:51 final size:49
Alignment explanation
Indices: 97840--97974 Score: 146
Period size: 51 Copynumber: 2.7 Consensus size: 49
97830 TCTTGGTTCC
*
97840 ATTTCCAAAACATTAATTTTTCTTAATCGGGGATACCCCAACTCCGATTTT
1 ATTTCCAAAACATCAATTTTTC--AATCGGGGATACCCCAACTCCGATTTT
* * * ** *
97891 ATTTCTAAAGCATCGATTTACCGCAATCGGGGATACTCCAACTCCGATTTT
1 ATTTCCAAAACATCAATTT--TTCAATCGGGGATACCCCAACTCCGATTTT
* *
97942 ATTTTCAAAACACCAATTTTTC-ATCGGGGATAC
1 ATTTCCAAAACATCAATTTTTCAATCGGGGATAC
97975 TCCGACCCCG
Statistics
Matches: 68, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
48 11 0.16
49 1 0.01
51 55 0.81
53 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (49 bp):
ATTTCCAAAACATCAATTTTTCAATCGGGGATACCCCAACTCCGATTTT
Found at i:98089 original size:79 final size:76
Alignment explanation
Indices: 97920--98114 Score: 266
Period size: 79 Copynumber: 2.5 Consensus size: 76
97910 ACCGCAATCG
* * *
97920 GGGATACTCCAACTCCGATTTTATTT-TCAAAACACCAATTTTTCATCGGGGATACTCCGACCCC
1 GGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTTCATCGAGGATACTCCAACCCC
97984 GTTATTTTCGAA
65 GTTATTTTCGAA
* * * *
97996 GGGATACTCCAACCCCGGTTTTATTTCTAAAATATCAATTTTTCATAATCGAGGATACTCCAATC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTC---ATCGAGGATACTCCAACC
*
98061 CTGTTATTTTCGAA
63 CCGTTATTTTCGAA
*
98075 GGGATACTCAAACCCCGATTTTATTTCTAAAACACCAATT
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATT
98115 CTCCACAATC
Statistics
Matches: 103, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
76 38 0.37
77 1 0.01
79 64 0.62
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (76 bp):
GGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCATCGAGGATACTCCAACCCCG
TTATTTTCGAA
Found at i:98245 original size:28 final size:29
Alignment explanation
Indices: 98166--98246 Score: 96
Period size: 28 Copynumber: 2.8 Consensus size: 29
98156 AACACTAATT
* *
98166 TTTCACAATCGGGGATACTCCAAACTCGTTA
1 TTTCACAA--GGGGATACTCCAACCTAGTTA
98197 TTTCATCAA--GGATACTCCAACCTAGTTA
1 TTTCA-CAAGGGGATACTCCAACCTAGTTA
98225 TTTC-CAAGGGGATACTCCAACC
1 TTTCACAAGGGGATACTCCAACC
98247 CCGGCTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
26 3 0.07
28 34 0.76
31 5 0.11
32 3 0.07
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (29 bp):
TTTCACAAGGGGATACTCCAACCTAGTTA
Found at i:98298 original size:51 final size:51
Alignment explanation
Indices: 98233--98350 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
98223 TATTTCCAAG
* *
98233 GGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATCA
1 GGGATACTCCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCA
** * *
98284 GGGATAC-CTCAACCCCGACCTTATTTTTAAAATATTGATTTCTCATAATTA
1 GGGATACTC-CAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCA
98335 GGGATACTCCAACCCC
1 GGGATACTCCAACCCC
98351 ATTATTTTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 1 0.02
51 57 0.97
52 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
GGGATACTCCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCA
Found at i:101296 original size:13 final size:13
Alignment explanation
Indices: 101278--101309 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
101268 TACATTTCTT
101278 AATGTATCGATAC
1 AATGTATCGATAC
101291 AATGTATCGATAC
1 AATGTATCGATAC
*
101304 ATTGTA
1 AATGTA
101310 CCATGTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:101373 original size:13 final size:13
Alignment explanation
Indices: 101355--101381 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
101345 TGCCAGTTTC
101355 ATGTATCGATACA
1 ATGTATCGATACA
101368 ATGTATCGATACA
1 ATGTATCGATACA
101381 A
1 A
101382 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:103621 original size:2 final size:2
Alignment explanation
Indices: 103614--103659 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
103604 ATCAAGCATA
* *
103614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
103655 AT AT A
1 AT AT A
103660 ACATAAACTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:105744 original size:20 final size:22
Alignment explanation
Indices: 105702--105747 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
105692 TATAGTAAAT
*
105702 ATATATGTAATAATATACGTAA
1 ATATATGTAATAATATACATAA
*
105724 ATATATGT-ATATTATA-ATAA
1 ATATATGTAATAATATACATAA
105744 ATAT
1 ATAT
105748 CCATATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
22 8 0.36
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (22 bp):
ATATATGTAATAATATACATAA
Found at i:105849 original size:13 final size:13
Alignment explanation
Indices: 105817--105841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
105807 ATATTATAAT
105817 ATATTTACAATAC
1 ATATTTACAATAC
105830 ATATTTACAATA
1 ATATTTACAATA
105842 TTATTTTATA
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:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATTTACAATAC
Found at i:108834 original size:2 final size:2
Alignment explanation
Indices: 108827--108859 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
108817 AGTTTGTCAT
108827 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
108860 AGTAAAAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:108850 original size:15 final size:15
Alignment explanation
Indices: 108830--108860 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
108820 TTGTCATTAT
108830 ATATATATATATATA
1 ATATATATATATATA
108845 ATATATATATATATA
1 ATATATATATATATA
108860 A
1 A
108861 GTAAAAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:113469 original size:2 final size:2
Alignment explanation
Indices: 113462--113497 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
113452 ATAATGTGTA
113462 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
113498 CACCCATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116165 original size:21 final size:22
Alignment explanation
Indices: 116139--116191 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
116129 TGGACATCTC
**
116139 AAAATGCATGGAACATGGCA-A
1 AAAATGCACAGAACATGGCATA
116160 AAAATGCACAGAACATGGCATA
1 AAAATGCACAGAACATGGCATA
116182 AAAATGCACA
1 AAAATGCACA
116192 AATATGGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.51, C:0.17, G:0.19, T:0.13
Consensus pattern (22 bp):
AAAATGCACAGAACATGGCATA
Found at i:117096 original size:20 final size:20
Alignment explanation
Indices: 117071--117146 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
117061 AAAAACCTAG
117071 AATGTATCGATACAATGAGA
1 AATGTATCGATACAATGAGA
*
117091 AATGTATCAATACAATTGTTAG-
1 AATGTATCGATACAA-TG--AGA
* * *
117113 CATGTATCGATACATTTA-A
1 AATGTATCGATACAATGAGA
117132 TAATGTATCGATACA
1 -AATGTATCGATACA
117147 TTTCCTTAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.02
20 27 0.60
21 3 0.07
22 12 0.27
23 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:121352 original size:27 final size:27
Alignment explanation
Indices: 121297--121352 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
121287 AATTATAGTT
* **
121297 GAAAGGTGGGGTTGAAGTATCCCTTTG
1 GAAAGATGGGGTTGAAGTATCCCCGTG
121324 GAAAGATGGGGTT-AGAGTATCCCCGTG
1 GAAAGATGGGGTTGA-AGTATCCCCGTG
121351 GA
1 GA
121353 TGACAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.25, C:0.12, G:0.38, T:0.25
Consensus pattern (27 bp):
GAAAGATGGGGTTGAAGTATCCCCGTG
Found at i:123868 original size:20 final size:20
Alignment explanation
Indices: 123845--123898 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
123835 CATTTCAAGC
* *
123845 ATGTATCGATACATTCAGTT
1 ATGTATCGATACATTAACTT
*
123865 ATGTATCAATACATTAACTT
1 ATGTATCGATACATTAACTT
*
123885 ATGTTATTGATACA
1 ATG-TATCGATACA
123899 AGTTGTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTAACTT
Found at i:123975 original size:20 final size:21
Alignment explanation
Indices: 123938--123976 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
123928 TGGGACCTTT
*
123938 TATCGATGCATGGTAGGCATG
1 TATCGATACATGGTAGGCATG
123959 TATCGATACAT-GTAGGCA
1 TATCGATACATGGTAGGCA
123977 AAAATATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (21 bp):
TATCGATACATGGTAGGCATG
Found at i:130610 original size:165 final size:164
Alignment explanation
Indices: 130051--130691 Score: 662
Period size: 166 Copynumber: 3.9 Consensus size: 164
130041 TTTCTTCTTT
* * * ** * *
130051 GTAAATTTTTTGAGAGGATTTTCATTAG-TTAAAATTTTTAAAATTCATCAAATATTATTATTTA
1 GTAATTTTTTTGGGAGGATTTTC-TTGGTTTTTAATTTTTAAAATTCATAAAATATCATTATTTA
* * * * * *
130115 TTTTATAATAAATCAGTTTTAAAAAATTTATTCACTTTCATAAGTTTTTAAATTTTTTTCTTGAA
65 TTTTATAATAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTTAAATTTTTTCCTTAAA
* * *
130180 ATTCTT-TTCTTTTCGAAAAACAG-AGTTTTCTCTTCC
130 ATTCTTCTT-TTTTCGAAATAC-GTTGTTTTCACTT-C
* * * *
130216 GTAAATTTTTTCGAGG-GGATTTTTCTTGGTTTCTAATTTTTAAAA-TCTATCAAATATTATTAT
1 GT-AATTTTTTTG-GGAGGA-TTTTCTTGGTTTTTAATTTTTAAAATTC-ATAAAATATCATTAT
* * * *
130279 TTATTTT-TAATAAATCAATTTTGAAAAATTAACTCATCTTCATGAGTTTTTAAATTTTTTCCTT
62 TTATTTTATAATAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTTAAATTTTTTCCTT
* * * *
130343 AAAATTCTTTTTTTTTCAAAATACGTTATTTTTTACTTC
127 AAAATTCTTCTTTTTTCGAAATACGTT-GTTTTCACTTC
* * *
130382 GTAA-----TTCGGAGGGATTTCTCTCT-GTTTTTAGTTTTTAAAATTAATAAAATATCATTATT
1 GTAATTTTTTTGGGA-GGATTT-TCT-TGGTTTTTAATTTTTAAAATTCATAAAATATCATTATT
* * *
130441 TATTTCATATTAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTTGAA-TTTTTCCTTA
63 TATTTTATAATAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTTAAATTTTTTCCTTA
*
130505 AAATTCTTCTTTTTCCGAAATACGTTGTTTTCGACTTC
128 AAATTCTTCTTTTTTCGAAATACGTTGTTTTC-ACTTC
* *
130543 GTAATTTTTTTGGGAGAATATTTCTTGGTTTTTAATTTTTAAAATTCATAAAATAACATTATTTA
1 GTAATTTTTTTGGGAGGAT-TTTCTTGGTTTTTAATTTTTAAAATTCATAAAATATCATTATTTA
** * *
130608 TTTTATCTTAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTTGAATTCTTTT-CTTGA
65 TTTTATAATAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTTAAATT-TTTTCCTTAA
*
130672 AATTCTCTTTTTTTTCGAAA
129 AATTCT-TCTTTTTTCGAAA
130692 AATTGAGTTT
Statistics
Matches: 401, Mismatches: 50, Indels: 48
0.80 0.10 0.10
Matches are distributed among these distances:
159 2 0.00
160 8 0.02
161 82 0.20
162 43 0.11
164 1 0.00
165 96 0.24
166 104 0.26
167 65 0.16
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (164 bp):
GTAATTTTTTTGGGAGGATTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATATCATTATTTAT
TTTATAATAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTTAAATTTTTTCCTTAAAA
TTCTTCTTTTTTCGAAATACGTTGTTTTCACTTC
Found at i:130685 original size:328 final size:329
Alignment explanation
Indices: 130085--130692 Score: 802
Period size: 328 Copynumber: 1.9 Consensus size: 329
130075 TTAGTTAAAA
* * * * *
130085 TTTTTAAAATTCATCAAATATTATTATTTATTTTATAATAAATCAGTTTTAAAAAATTTATTCAC
1 TTTTTAAAATTAATAAAATATCATTATTTATTTCATAATAAATCAGTTTTAAAAAATTAATTCAC
* * * *
130150 TTTCATAAGTTTTTAAATTTTTTTCTTGAAATTCTTTTCTTTTCGAAAAACAGAGTTTTCTCTTC
66 TTTCATAAGTTTTTAAATTTTTTCCTTAAAATTCTTTTCTTTCCGAAAAACAGAGTTTTCACTTC
* * * **
130215 CGTAAATTTTTTCGAGGGGATTTTTCTTGGTTTCTAATTTTTAAAATCTATCAAATATTATTATT
131 CGTAAATTTTTTCGAGGGAATATTTCTTGGTTTCTAATTTTTAAAATCTATAAAATAACATTATT
130280 TATTTTTAATAAATCAATTTTGAAAAATTAACTCATCTTCATGAGTTTTTAAATTTTTTCCTTAA
196 TATTTTTAATAAATCAATTTTGAAAAATTAACTCATCTTCATGAGTTTTTAAATTTTTTCCTTAA
130345 AATTCTTTTTTTTTC-AAAATACGTTATTTTTTACTTCGTAATTCGGAGGGATTTCTCTCTGTTT
261 AATTCTTTTTTTTTCGAAAATACGTTATTTTTTACTTCGTAATTCGGAGGGATTTCTCTCTGTTT
130409 TTAG
326 TTAG
* * *
130413 TTTTTAAAATTAATAAAATATCATTATTTATTTCATATTAAATCAGTTTTTAAAAATTAATTCAT
1 TTTTTAAAATTAATAAAATATCATTATTTATTTCATAATAAATCAGTTTTAAAAAATTAATTCAC
* * * *
130478 TTTCATGAGTTTTTGAA-TTTTTCCTTAAAATTCTTCTT-TTTCCGAAATAC-GTTGTTTTCGAC
66 TTTCATAAGTTTTTAAATTTTTTCCTTAAAATTCTT-TTCTTTCCGAAAAACAG-AGTTTTC-AC
* *
130540 TT-CGT-AATTTTTTTG-GGAGAATATTTCTTGGTTTTTAATTTTTAAAAT-TCATAAAATAACA
128 TTCCGTAAATTTTTTCGAGG-GAATATTTCTTGGTTTCTAATTTTTAAAATCT-ATAAAATAACA
** * * * * *
130601 TTATTTATTTTATCTTAAATCAGTTTTTAAAAATTAATTCATTTTCATGAGTTTTTGAATTCTTT
191 TTATTTATTTT-TAATAAATCAATTTTGAAAAATTAACTCATCTTCATGAGTTTTTAAATT-TTT
*
130666 T-CTTGAAATTCTCTTTTTTTTCGAAAA
254 TCCTTAAAATTCT-TTTTTTTTCGAAAA
130693 ATTGAGTTTT
Statistics
Matches: 240, Mismatches: 31, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
325 3 0.01
326 56 0.23
327 87 0.36
328 90 0.38
329 4 0.02
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.51
Consensus pattern (329 bp):
TTTTTAAAATTAATAAAATATCATTATTTATTTCATAATAAATCAGTTTTAAAAAATTAATTCAC
TTTCATAAGTTTTTAAATTTTTTCCTTAAAATTCTTTTCTTTCCGAAAAACAGAGTTTTCACTTC
CGTAAATTTTTTCGAGGGAATATTTCTTGGTTTCTAATTTTTAAAATCTATAAAATAACATTATT
TATTTTTAATAAATCAATTTTGAAAAATTAACTCATCTTCATGAGTTTTTAAATTTTTTCCTTAA
AATTCTTTTTTTTTCGAAAATACGTTATTTTTTACTTCGTAATTCGGAGGGATTTCTCTCTGTTT
TTAG
Found at i:131693 original size:20 final size:20
Alignment explanation
Indices: 131668--131814 Score: 87
Period size: 20 Copynumber: 6.8 Consensus size: 20
131658 TTTTTACCCA
131668 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * *
131688 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
* * *
131708 AATGTATTGATGCATTATTC
1 AATGTATCGATACATTTTTC
* *
131728 AATGTGTTGATACATTCTATTTTTTTACC
1 AATGTATCGAT--A--C-A--TTTTT--C
131757 TAGATGTATCGATACATTTTTC
1 -A-ATGTATCGATACATTTTTC
* * *
131779 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
*
131799 AATGTATTGATACATT
1 AATGTATCGATACATT
131815 GAATACATTC
Statistics
Matches: 97, Mismatches: 19, Indels: 22
0.70 0.14 0.16
Matches are distributed among these distances:
20 71 0.73
21 1 0.01
22 1 0.01
24 6 0.06
25 1 0.01
26 1 0.01
27 5 0.05
29 2 0.02
30 1 0.01
31 8 0.08
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:131791 original size:51 final size:51
Alignment explanation
Indices: 131709--131893 Score: 178
Period size: 51 Copynumber: 3.7 Consensus size: 51
131699 ACATGTATGA
* * * * * *
131709 ATGTATTGATGCATTATTCAATGTGTTGATACATTCTATTTTTTTACCTAG
1 ATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTTTACCTAG
* *** * *
131760 ATGTATCGATACATTTTTCAATGTATCGATACA-TGTATGAATGTA--TTG
1 ATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTTTACCTAG
** * * * *
131808 ATACATTGAATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAG
1 ATGTATCG-ATACATTTTTCAATGTATCGATACATTCTATCTTTTTACCTAG
131860 ATGTATCGATACATTTTTCAATGTATCGATACAT
1 ATGTATCGATACATTTTTCAATGTATCGATACAT
131894 CTAGTTAAAA
Statistics
Matches: 103, Mismatches: 27, Indels: 8
0.75 0.20 0.06
Matches are distributed among these distances:
48 7 0.07
49 24 0.23
50 13 0.13
51 53 0.51
52 6 0.06
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (51 bp):
ATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTTTACCTAG
Found at i:135974 original size:13 final size:13
Alignment explanation
Indices: 135956--136012 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
135946 CATAAAGTGT
135956 TGTATCGATACAA
1 TGTATCGATACAA
135969 TGTATCGATACATAA
1 TGTATCGATAC--AA
135984 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
136001 TGTATCGATACA
1 TGTATCGATACA
136013 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:135991 original size:32 final size:32
Alignment explanation
Indices: 135936--136033 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
135926 TTCAATGATT
135936 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
135969 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
136001 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
136033 T
1 T
136034 ATAAGCTACT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:135993 original size:19 final size:18
Alignment explanation
Indices: 135934--136031 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
135924 TTTTCAATGA
135934 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
135953 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
135969 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
135985 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
136001 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
136017 TTTTGTATCGATACA
1 -TTTGTATCGATACA
136032 ATATAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:136090 original size:13 final size:13
Alignment explanation
Indices: 136072--136096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
136062 ACATTTCAAA
136072 TGTATCGATACAT
1 TGTATCGATACAT
136085 TGTATCGATACA
1 TGTATCGATACA
136097 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:137542 original size:13 final size:13
Alignment explanation
Indices: 137524--137549 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
137514 TACACCAAGT
137524 ATGTATCGATACA
1 ATGTATCGATACA
137537 ATGTATCGATACA
1 ATGTATCGATACA
137550 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:137547 original size:32 final size:33
Alignment explanation
Indices: 137506--137569 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
137496 TAGCCAAACT
* **
137506 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
137538 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
137570 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:139814 original size:21 final size:22
Alignment explanation
Indices: 139768--139812 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
139758 TTGCAAGATG
139768 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
139790 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
139810 AAA
1 AAA
139813 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:141636 original size:15 final size:15
Alignment explanation
Indices: 141616--141646 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
141606 TAAAAATGTC
*
141616 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
141631 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
141646 C
1 C
141647 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:143744 original size:13 final size:13
Alignment explanation
Indices: 143726--143751 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
143716 ACATTTTTCT
143726 TTGTATCGATACA
1 TTGTATCGATACA
143739 TTGTATCGATACA
1 TTGTATCGATACA
143752 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:143915 original size:20 final size:20
Alignment explanation
Indices: 143872--143917 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
143862 AAATCTTTTG
143872 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
143893 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
143913 CAAAA
1 CAAAA
143918 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:146321 original size:13 final size:13
Alignment explanation
Indices: 146303--146328 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
146293 TACACCAAGT
146303 ATGTATCGATACA
1 ATGTATCGATACA
146316 ATGTATCGATACA
1 ATGTATCGATACA
146329 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:146326 original size:32 final size:33
Alignment explanation
Indices: 146285--146348 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
146275 TAGCCAAACT
* **
146285 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
146317 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
146349 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:157297 original size:29 final size:29
Alignment explanation
Indices: 157230--157550 Score: 229
Period size: 30 Copynumber: 10.7 Consensus size: 29
157220 TCACCCTTCA
157230 AAAGCCCACAAGTCAGTGGCATCTTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTT-C
157260 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
157289 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
157316 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * *
157346 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
157375 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * * *
157405 TTTTGTAAGCTCACAACTCCGTAGCACTCTTTTTCC
1 -----AAAGCCCACAAGTCAGTGGCA-TCTTTTT-C
* * * *
157441 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ---AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
157473 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
157502 AAAGCCCATAAGTCAGTAGCAATC--TTTA
1 AAAGCCCACAAGTCAGTGGC-ATCTTTTTC
157530 AAAGCCCACAAGTCAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
157551 ACCTTCAAAA
Statistics
Matches: 240, Mismatches: 40, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
27 23 0.10
28 41 0.17
29 51 0.21
30 75 0.31
32 1 0.00
33 5 0.02
34 18 0.08
35 25 0.10
36 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:157332 original size:86 final size:88
Alignment explanation
Indices: 157230--157550 Score: 278
Period size: 86 Copynumber: 3.6 Consensus size: 88
157220 TCACCCTTCA
*
157230 AAAGCCCACAAGTCAGTGGCATCTTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGTC
1 AAAGCCCACAAGTCAGTAGCATCTTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGTC
157295 CACAAGTCAGTGGCAACC-TTC-
66 CACAAGTCAGTGGCAACCTTTCT
* * * * * * *
157316 AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGGCATCTTTTCCAAAGTC
1 AAAGCCCACAAGTCAGTAGCATCTTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGTC
* *
157381 CACAACTCCGTGGC-ACTCTTTTTCTTTT
66 CACAAGTCAGTGGCAAC-C--TTTC---T
* * * * * * * *
157409 GTAAGCTCACAACTCCGTAGCACTCTTTTTCCTTTTAAGCCCACAAGTTAGTGGCACCCTTTTCA
1 -AAAGCCCACAAGTCAGTAGCA-TCTTTTTCC---AAAGCCCACAAGTCAGTGGCATCTTTTTC-
* *
157474 AAAGCCCACAAGTCAGTGGCAACCTTT-A
60 AAAGTCCACAAGTCAGTGGCAACCTTTCT
* *
157502 AAAGCCCATAAGTCAGTAGCAATC--TTT-AAAAGCCCACAAGTCAGTGGCA
1 AAAGCCCACAAGTCAGTAGC-ATCTTTTTCCAAAGCCCACAAGTCAGTGGCA
157551 ACCTTCAAAA
Statistics
Matches: 186, Mismatches: 33, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
85 2 0.01
86 91 0.49
89 3 0.02
90 3 0.02
92 17 0.09
93 1 0.01
94 16 0.09
95 7 0.04
97 3 0.02
98 23 0.12
99 18 0.10
100 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (88 bp):
AAAGCCCACAAGTCAGTAGCATCTTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGTC
CACAAGTCAGTGGCAACCTTTCT
Found at i:157454 original size:34 final size:35
Alignment explanation
Indices: 157380--157454 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
157370 TTTCCAAAGT
* *
157380 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
*
157415 TCACAACTCCGTAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
157449 CCACAA
1 CCACAA
157455 GTTAGTGGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.35
Consensus pattern (35 bp):
CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
Found at i:157471 original size:34 final size:35
Alignment explanation
Indices: 157380--157471 Score: 105
Period size: 35 Copynumber: 2.7 Consensus size: 35
157370 TTTCCAAAGT
* *
157380 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCAGTGGCACTCTTTTTCCTTTGTAAGC
* * *
157415 TCACAACTCCGTAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTCAGTGGCACTCTTTTTCCTTTGTAAGC
* * *
157449 CCACAAGTTAGTGGCACCCTTTT
1 CCACAACTCAGTGGCACTCTTTT
157472 CAAAAGCCCA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
34 22 0.46
35 26 0.54
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.36
Consensus pattern (35 bp):
CCACAACTCAGTGGCACTCTTTTTCCTTTGTAAGC
Found at i:157514 original size:28 final size:28
Alignment explanation
Indices: 157445--157596 Score: 173
Period size: 28 Copynumber: 5.3 Consensus size: 28
157435 TTTTCCTTTT
* *
157445 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTT-AA
157475 AAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
* * *
157503 AAGCCCATAAGTCAGTAGCAATCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
*
157531 AAGCCCACAAGTCAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
* *
157559 AAGCACACAAGT-TGAT-GCAAACCTTTCAA
1 AAGCCCACAAGTCAG-TGGC-AACCTTT-AA
157588 AAGCCCACA
1 AAGCCCACA
157597 CAAGTTGGTG
Statistics
Matches: 106, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
27 3 0.03
28 69 0.65
29 13 0.12
30 21 0.20
ACGTcount: A:0.37, C:0.28, G:0.16, T:0.19
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTTAA
Found at i:157685 original size:48 final size:49
Alignment explanation
Indices: 157616--157955 Score: 400
Period size: 48 Copynumber: 7.0 Consensus size: 49
157606 GGCGTCTTCT
* * *
157616 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-GTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * *
157664 TTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCA-CTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * *
157712 TTTAAGTCCAATATCGTTGGCCTTGAATCCGCATATTGGCGCTTTTGGCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC-CTT--CATC
*
157764 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * *
157813 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGTACC-TCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* *
157861 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * *
157909 TTTAAGACCAATGTCGCCGGCCTTGAATCAGCACATTGTCACCTTCA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
157956 AGTCTAACTG
Statistics
Matches: 248, Mismatches: 37, Indels: 13
0.83 0.12 0.04
Matches are distributed among these distances:
47 3 0.01
48 158 0.64
49 42 0.17
50 2 0.01
51 2 0.01
52 41 0.17
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (49 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
Found at i:158599 original size:13 final size:13
Alignment explanation
Indices: 158581--158637 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
158571 CATAAAGTGT
158581 TGTATCGATACAA
1 TGTATCGATACAA
158594 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
158609 GTGTTGTTTCGATACAA
1 ----TGTATCGATACAA
158626 TGTATCGATACA
1 TGTATCGATACA
158638 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:158621 original size:32 final size:32
Alignment explanation
Indices: 158561--158661 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
158551 TTCAACGATT
158561 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
*
158594 TGTATCGATACATAAGTGTTGTTTCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
158626 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
158658 TGTA
1 TGTA
158662 AGCTACTGCC
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 52 0.80
33 13 0.20
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Done.