Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014485.1 Kokia drynarioides strain JFW-HI SEQ_129524, whole genome shotgun sequence
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: 258484
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:9008 original size:29 final size:29
Alignment explanation
Indices: 8965--9235 Score: 116
Period size: 29 Copynumber: 9.2 Consensus size: 29
8955 AAAACGGTGA
* *
8965 TTTTGGATGTTTCGAGGGTAAAATGATAAA
1 TTTTGGAT-ATTCGAGGGTAAAATGATAAT
*
8995 TTTTGGATATTCGAAGGTAAAAATG-TAAT
1 TTTTGGATATTCGAGGGT-AAAATGATAAT
* *
9024 TTTTGGAATTTTCG-GCGTAAAAAAT-ATAAT
1 TTTTGG-ATATTCGAGGGT--AAAATGATAAT
* * *
9054 TTTTGGACA-CCCAGGGGTAAAATGATAAT
1 TTTTGGATATTCGA-GGGTAAAATGATAAT
* * *
9083 TTTTGAATGTTC-AGGGGTAAAATGGTAAT
1 TTTTGGATATTCGA-GGGTAAAATGATAAT
* * * *
9112 TTTTGAAAAGTTTG-GGGCCAAAAATG-TAAT
1 TTTTGGATA-TTCGAGGG--TAAAATGATAAT
* * *
9142 TTTTGGACATT-TAGGGGTAAAATGGTAAT
1 TTTTGGATATTCGA-GGGTAAAATGATAAT
* * *
9171 TTTTGGAAAGTTTG-GGGTCAAAATG-GAA-
1 TTTTGGATA-TTCGAGGGT-AAAATGATAAT
* *
9199 TTATGGAAAGTTCGAGGGTAAAAATG-TAAT
1 TTTTGGATA-TTCGAGGGT-AAAATGATAAT
9229 TTTTGGA
1 TTTTGGA
9236 AAGTATGGGG
Statistics
Matches: 189, Mismatches: 32, Indels: 40
0.72 0.12 0.15
Matches are distributed among these distances:
28 24 0.13
29 89 0.47
30 70 0.37
31 6 0.03
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.35
Consensus pattern (29 bp):
TTTTGGATATTCGAGGGTAAAATGATAAT
Found at i:9075 original size:88 final size:88
Alignment explanation
Indices: 8980--9177 Score: 222
Period size: 88 Copynumber: 2.2 Consensus size: 88
8970 GATGTTTCGA
* * * *
8980 GGGTAAAATGATAAATTTTGGATATTC-GAAGGTAAAAAT-GTAATTTTTG-GAATTTTCGGCGT
1 GGGTAAAATGATAATTTTTGGATATTCAG-AGGT-AAAATGGTAATTTTTGAAAAGTTT-GGCGC
9042 AAAAAATATAATTTTTGGACACCCAG
63 AAAAAATATAATTTTTGGACACCCAG
* * * * *
9068 GGGTAAAATGATAATTTTTGAATGTTCAGGGGTAAAATGGTAATTTTTGAAAAGTTTGGGGCCAA
1 GGGTAAAATGATAATTTTTGGATATTCAGAGGTAAAATGGTAATTTTTGAAAAGTTTGGCGCAAA
* ***
9133 AAATGTAATTTTTGGACATTTAG
66 AAATATAATTTTTGGACACCCAG
*
9156 GGGTAAAATGGTAATTTTTGGA
1 GGGTAAAATGATAATTTTTGGA
9178 AAGTTTGGGG
Statistics
Matches: 92, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
87 5 0.05
88 81 0.88
89 6 0.07
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (88 bp):
GGGTAAAATGATAATTTTTGGATATTCAGAGGTAAAATGGTAATTTTTGAAAAGTTTGGCGCAAA
AAATATAATTTTTGGACACCCAG
Found at i:9188 original size:88 final size:88
Alignment explanation
Indices: 9009--9410 Score: 312
Period size: 88 Copynumber: 4.5 Consensus size: 88
8999 GGATATTCGA
* * * * ***
9009 AGGTAAAAAT-GTAATTTTTGGAATTTTCGGCGTAAAAAATATAATTTTTGGACACCCAGGGGT-
1 AGGT-AAAATGGTAATTTTTGAAAGTTT-GGGGT-AAAAATGTAATTTTTGGACATTTAGGGGTA
* * *
9072 AAAATGATAATTTTT-GAATGTTCAGG
63 AAAATGGTAATTTTTGGAAAGTT-TGG
*
9098 -GGTAAAATGGTAATTTTTGAAAAGTTTGGGGCCAAAAATGTAATTTTTGGACATTTAGGGGT-A
1 AGGTAAAATGGTAATTTTTG-AAAGTTTGGGG-TAAAAATGTAATTTTTGGACATTTAGGGGTAA
9161 AAATGGTAATTTTTGGAAAGTTTGG
64 AAATGGTAATTTTTGGAAAGTTTGG
* * * **
9186 -GGTCAAAATGG-AATTATGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGA-AAGTATGGGGTT
1 AGGT-AAAATGGTAATTTTTGAAAGTTTG-GGGTAAAAATGTAATTTTTGGACATTTA-GGGG-T
9248 AAAAATGG-AA-TTTTGGAAAGTTTGG
62 AAAAATGGTAATTTTTGGAAAGTTTGG
* * * * *
9273 TGGTAAGAAT-GTAATTTTTGGAAGTTTTGGGGTTAAAAAAGGAA-TTTTGGAAAATTT-GAGGG
1 AGGTAA-AATGGTAATTTTTGAAAG-TTTGGGG-TAAAAATGTAATTTTTGG-ACATTTAG-GGG
*
9335 TAAAAAT-GTAATTTTTTG-AAGTTTTGG
61 TAAAAATGGTAATTTTTGGAAAG-TTTGG
* * * *
9362 AGTTAAAATTGAAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTG
1 AGGTAAAATGGTAATTTTTGAAAGTTT-GGGGTAAAAATGTAATTTTTG
9411 ATAGTTTTAG
Statistics
Matches: 259, Mismatches: 31, Indels: 46
0.77 0.09 0.14
Matches are distributed among these distances:
86 3 0.01
87 53 0.20
88 124 0.48
89 77 0.30
90 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (88 bp):
AGGTAAAATGGTAATTTTTGAAAGTTTGGGGTAAAAATGTAATTTTTGGACATTTAGGGGTAAAA
ATGGTAATTTTTGGAAAGTTTGG
Found at i:9246 original size:29 final size:29
Alignment explanation
Indices: 9010--9439 Score: 328
Period size: 30 Copynumber: 14.6 Consensus size: 29
9000 GATATTCGAA
*
9010 GGTAAAAATGTAATTTTTGG-AATTTTCGG
1 GGTAAAAATGTAATTTTTGGAAAGTTT-GG
* * * ****
9039 CGTAAAAAATATAATTTTTGGACACCCAGG
1 GGT-AAAAATGTAATTTTTGGAAAGTTTGG
* *
9069 GGT-AAAATGATAATTTTT-GAATGTTCAGG
1 GGTAAAAATG-TAATTTTTGGAAAGTT-TGG
*
9098 GGT-AAAATGGTAATTTTTGAAAAGTTTGG
1 GGTAAAAAT-GTAATTTTTGGAAAGTTTGG
* *
9127 GGCCAAAAATGTAATTTTTGGACA-TTTAGG
1 GG-TAAAAATGTAATTTTTGGAAAGTTT-GG
9157 GGT-AAAATGGTAATTTTTGGAAAGTTTGG
1 GGTAAAAAT-GTAATTTTTGGAAAGTTTGG
* * * *
9186 GGTCAAAATGGAA-TTATGGAAAGTTCGAG
1 GGTAAAAATGTAATTTTTGGAAAGTTTG-G
*
9215 GGTAAAAATGTAATTTTTGGAAAGTATGG
1 GGTAAAAATGTAATTTTTGGAAAGTTTGG
*
9244 GGTTAAAAATGGAA-TTTTGGAAAGTTTGG
1 GG-TAAAAATGTAATTTTTGGAAAGTTTGG
*
9273 TGGTAAGAATGTAATTTTTGG-AAGTTTTGG
1 -GGTAAAAATGTAATTTTTGGAAAG-TTTGG
* * *
9303 GGTTAAAAAAGGAA-TTTTGGAAAATTTGAG
1 GG-TAAAAATGTAATTTTTGGAAAGTTTG-G
*
9333 GGTAAAAATGTAATTTTTTG-AAGTTTTGG
1 GGTAAAAATGTAATTTTTGGAAAG-TTTGG
* * *
9362 AGTTAAAATTGAAATTTTTGG-AAGTTTGGG
1 -GGTAAAAATGTAATTTTTGGAAAGTTT-GG
*
9392 GGTAAAAATGTAATTTTT-GATAGTTTTAGG
1 GGTAAAAATGTAATTTTTGGAAAG-TTT-GG
* *
9422 GTTAAAAATGAAATTTTT
1 GGTAAAAATGTAATTTTT
9440 AAAAGTTCGG
Statistics
Matches: 321, Mismatches: 53, Indels: 53
0.75 0.12 0.12
Matches are distributed among these distances:
28 25 0.08
29 142 0.44
30 148 0.46
31 6 0.02
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
GGTAAAAATGTAATTTTTGGAAAGTTTGG
Found at i:9439 original size:59 final size:60
Alignment explanation
Indices: 9012--9439 Score: 355
Period size: 59 Copynumber: 7.3 Consensus size: 60
9002 TATTCGAAGG
* * * * * * ****
9012 TAAAAATGTAATTTTTGG-AATTTTCGGCGTAAAAAATATAATTTTTGGACACCCAGGGG-
1 TAAAAATGAAATTTTTGGAAAGTTTGGGGGT-AAAAATGTAATTTTTGGAAAGTTTGGGGT
* ** * *
9071 T-AAAATGATAATTTTT-GAATGTTCAGGGGT-AAAATGGTAATTTTTGAAAAGTTTGGGGC
1 TAAAAATGA-AATTTTTGGAAAGTTTGGGGGTAAAAAT-GTAATTTTTGGAAAGTTTGGGGT
* * * *
9130 CAAAAATGTAATTTTTGGACA-TTTAGGGGT-AAAATGGTAATTTTTGGAAAGTTTGGGG-
1 TAAAAATGAAATTTTTGGAAAGTTTGGGGGTAAAAAT-GTAATTTTTGGAAAGTTTGGGGT
* * * * * *
9188 TCAAAATGGAA-TTATGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTATGGGGT
1 TAAAAATGAAATTTTTGGAAAGTTTGGGGGTAAAAATGTAATTTTTGGAAAGTTTGGGGT
* * *
9247 TAAAAATGGAA-TTTTGGAAAGTTTGGTGGTAAGAATGTAATTTTTGG-AAGTTTTGGGGT
1 TAAAAATGAAATTTTTGGAAAGTTTGGGGGTAAAAATGTAATTTTTGGAAAG-TTTGGGGT
* * * * * *
9306 TAAAAAAGGAA-TTTTGGAAAATTTGAGGGTAAAAATGTAATTTTTTG-AAGTTTTGGAGT
1 TAAAAATGAAATTTTTGGAAAGTTTGGGGGTAAAAATGTAATTTTTGGAAAG-TTTGGGGT
* * *
9365 TAAAATTGAAATTTTTGG-AAGTTTGGGGGTAAAAATGTAATTTTT-GATAGTTTTAGGGT
1 TAAAAATGAAATTTTTGGAAAGTTTGGGGGTAAAAATGTAATTTTTGGAAAG-TTTGGGGT
9424 TAAAAATGAAATTTTT
1 TAAAAATGAAATTTTT
9440 AAAAGTTCGG
Statistics
Matches: 306, Mismatches: 51, Indels: 24
0.80 0.13 0.06
Matches are distributed among these distances:
57 12 0.04
58 61 0.20
59 219 0.72
60 14 0.05
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (60 bp):
TAAAAATGAAATTTTTGGAAAGTTTGGGGGTAAAAATGTAATTTTTGGAAAGTTTGGGGT
Found at i:11236 original size:35 final size:34
Alignment explanation
Indices: 11176--11243 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 34
11166 TTTTAATTTA
*
11176 AAAATAAATTTAAATTTAAAGTAAATCCAAACTC
1 AAAATAAATTTAAATTTAAAATAAATCCAAACTC
* * *
11210 AAAATGAATTTGAATTTTAAAATAAATTCAAACT
1 AAAATAAATTT-AAATTTAAAATAAATCCAAACT
11244 TATTTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 10 0.34
35 19 0.66
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.32
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATCCAAACTC
Found at i:20957 original size:35 final size:35
Alignment explanation
Indices: 20891--20962 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
20881 TTATAATCTC
* * *
20891 AAAACATTGAAAGATTAAAATTGAAATTTTACCAT
1 AAAACAATGAAAGATTAAAATTGAAAATTTACAAT
*
20926 AAAACAATGAAAATATTAAAATT-AAAATTTACAAT
1 AAAACAATG-AAAGATTAAAATTGAAAATTTACAAT
20961 AA
1 AA
20963 TCTTTTCATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 20 0.62
36 12 0.38
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (35 bp):
AAAACAATGAAAGATTAAAATTGAAAATTTACAAT
Found at i:26924 original size:17 final size:19
Alignment explanation
Indices: 26893--26941 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 19
26883 TTCACCCCGA
*
26893 AAAATTAAATTTAAGAAA-
1 AAAATTAATTTTAAGAAAC
*
26911 TAAA-TAATTTTAAGAAAC
1 AAAATTAATTTTAAGAAAC
26929 AAAATTAATTTTA
1 AAAATTAATTTTA
26942 TTAAACAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 12 0.46
18 6 0.23
19 8 0.31
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAATTAATTTTAAGAAAC
Found at i:26933 original size:18 final size:18
Alignment explanation
Indices: 26902--26956 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 18
26892 AAAAATTAAA
*
26902 TTTAAGAAA-TAAATAAT
1 TTTAAGAAACAAAATAAT
26919 TTTAAGAAACAAAATTAAT
1 TTTAAGAAACAAAA-TAAT
** *
26938 TTTATTAAACAATATAAT
1 TTTAAGAAACAAAATAAT
26956 T
1 T
26957 ATATTCCGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 9 0.28
18 8 0.25
19 15 0.47
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (18 bp):
TTTAAGAAACAAAATAAT
Found at i:30522 original size:20 final size:19
Alignment explanation
Indices: 30482--30522 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
30472 AGAGGGAAAG
* *
30482 TGGGAGAAAGTAAGAGTTT
1 TGGGAGAAAATAAAAGTTT
30501 TGGGAGAAAATAAAATGTTT
1 TGGGAGAAAATAAAA-GTTT
30521 TG
1 TG
30523 AGGGTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (19 bp):
TGGGAGAAAATAAAAGTTT
Found at i:31624 original size:2 final size:2
Alignment explanation
Indices: 31617--31658 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
31607 TTCACTATCC
31617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31658 A
1 A
31659 AGTGAGTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37849 original size:454 final size:459
Alignment explanation
Indices: 36891--37993 Score: 1816
Period size: 454 Copynumber: 2.4 Consensus size: 459
36881 CATACTATGA
* *
36891 ATGTTGAGATCTACTAGTTGCTTGCTCAAGAATCTACTAACTTACACACGGAAAAACAATCGTAC
1 ATGTTGAGATCTACTAGTTGCTTGCTCAAGAATCTACTAACCTACACACGAAAAAACAAT-GTAC
* * * *
36956 GTTAAGCAAATGGCTCAATGGTAAACTATGATTCAAATTAACATAAAAATGAAAATGAAAATGGA
65 GCTAAGCAAATTGCTCAGTGGTAAACTATGATTCAAATTAACATAAAAATGAAAATGCAAATGGA
*
37021 TACAATTAAGTCAAGTTTATTTCATACAAAATTTCTTGTCATTCATCTCAACTA---CAAATTTT
130 TACAATTAAGTCAAGTTTATTTCATACAAAATTTCATGTCATTCATCTCAACTACTTCAAATTTT
*
37083 AAGTGGCATACTTATGCATATCTCAATTTCTTACTCAAGTACATGATGATGCTAACCTATTCATT
195 AAGTAGCATACTTATGCATATCTCAATTTCTTACTCAAGTACATGATGATGCTAACCTATTCATT
*
37148 TGCATTTGCATTTTCATTTTCATTTCCATACCTTATCCATATAAATAAACTCATCAACATGTCAC
260 TGCATTTGCATTTTCATTTTCATTTCCATACCTTATCCATATAAATAAACACATCAACATGTCAC
*
37213 AATCATAACAACAAATTTTTATCATATAGTACATATTCATATTTACTTAATTCCAAATATCATAA
325 AAGCATAACAACAAATTTTTATCATATAGTACATATTCATATTTACTTAATTCCAAATATCATAA
* *
37278 TAAAAATCTTCGAGACTATAAGTTAGGTTCTTGATCTATTAGCCCTCTGGGCTCATTTTCAATCC
390 TAAAAATCTTCGAGACTATAAGTTAGGTTCTTGATCTATTAGCCCTCGGGGCTCACTTTCAATCC
37343 TCTGG
455 TCTGG
* * * *
37348 ATGTTGAGATCTACTAGTTGCTTGCTCAAGAATCTACTAATCTACACACGAAAAAATAACTGCAT
1 ATGTTGAGATCTACTAGTTGCTTGCTCAAGAATCTACTAACCTACACACGAAAAAACAA-TGTAC
37413 GCTAAGCAAATTGCTCAGTGGTAAACTATGATTCAAATTAACATAAAAATGAAAATGCAAATGGA
65 GCTAAGCAAATTGCTCAGTGGTAAACTATGATTCAAATTAACATAAAAATGAAAATGCAAATGGA
* *
37478 TACAATTTAGTCAAGTTTATTTCATATAAAATTTCATGTCATTCATCTCAACTACTTCAAATTTT
130 TACAATTAAGTCAAGTTTATTTCATACAAAATTTCATGTCATTCATCTCAACTACTTCAAATTTT
37543 AAGTAGCATACTTATGCATATCTCAATTTCTTACTCAAGTACATGATGATGCTAA-C-A-T-A-T
195 AAGTAGCATACTTATGCATATCTCAATTTCTTACTCAAGTACATGATGATGCTAACCTATTCATT
* *
37603 T-CATTTGCATTTTCATTTTCATTTCCATACCTTATCTATATAAATAAACACATTAACATGTCAC
260 TGCATTTGCATTTTCATTTTCATTTCCATACCTTATCCATATAAATAAACACATCAACATGTCAC
* * *
37667 AAGCATAACAACAATTTTTTTATCATGTAGTACATATTCATATTTACTTAATTCCAGATATCATA
325 AAGCATAACAACAA-ATTTTTATCATATAGTACATATTCATATTTACTTAATTCCAAATATCATA
* * *
37732 ATAACAATCTTCGAGTCTGTAAGTTAGGTT-TTGATCTATTAGCCCTCGGGGCTCACTTTCAATC
389 ATAAAAATCTTCGAGACTATAAGTTAGGTTCTTGATCTATTAGCCCTCGGGGCTCACTTTCAATC
37796 CTCTGG
454 CTCTGG
*
37802 ATGTTGAGATCTACTAGTTGCTTGCTCAAGAATCTACTAACCTACACAC-AGAAAAACAGTTGTA
1 ATGTTGAGATCTACTAGTTGCTTGCTCAAGAATCTACTAACCTACACACGA-AAAAACA-ATGTA
* *
37866 CGCTAAGCAAATTGCTTAGTGGTAAACTATGGTTCAAATTAACAT-AAAATGAAAATGCAAATGG
64 CGCTAAGCAAATTGCTCAGTGGTAAACTATGATTCAAATTAACATAAAAATGAAAATGCAAATGG
37930 ATACAATTAAGTCAAGTTTATTTCATACAAAATTTCATGTCATTCATCTCAACTACTTCAAATT
129 ATACAATTAAGTCAAGTTTATTTCATACAAAATTTCATGTCATTCATCTCAACTACTTCAAATT
37994 AACATAGAAA
Statistics
Matches: 604, Mismatches: 35, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
453 82 0.14
454 210 0.35
455 76 0.13
456 1 0.00
457 170 0.28
458 2 0.00
459 1 0.00
460 62 0.10
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (459 bp):
ATGTTGAGATCTACTAGTTGCTTGCTCAAGAATCTACTAACCTACACACGAAAAAACAATGTACG
CTAAGCAAATTGCTCAGTGGTAAACTATGATTCAAATTAACATAAAAATGAAAATGCAAATGGAT
ACAATTAAGTCAAGTTTATTTCATACAAAATTTCATGTCATTCATCTCAACTACTTCAAATTTTA
AGTAGCATACTTATGCATATCTCAATTTCTTACTCAAGTACATGATGATGCTAACCTATTCATTT
GCATTTGCATTTTCATTTTCATTTCCATACCTTATCCATATAAATAAACACATCAACATGTCACA
AGCATAACAACAAATTTTTATCATATAGTACATATTCATATTTACTTAATTCCAAATATCATAAT
AAAAATCTTCGAGACTATAAGTTAGGTTCTTGATCTATTAGCCCTCGGGGCTCACTTTCAATCCT
CTGG
Found at i:38102 original size:89 final size:89
Alignment explanation
Indices: 37898--38082 Score: 345
Period size: 89 Copynumber: 2.1 Consensus size: 89
37888 TAAACTATGG
* *
37898 TTCAAATTAACATA-AAATGAAAATGCAAATGGATACAATTAAGTCAAGTTTATTTCATACAAAA
1 TTCAAATTAACATAGAAATGAAAATGCAAATGGAAACAATTAAATCAAGTTTATTTCATACAAAA
37962 TTTCATGTCATTCATCTCAACTAC
66 TTTCATGTCATTCATCTCAACTAC
37986 TTCAAATTAACATAGAAATGAAAATGCAAATGGAAACAATTAAATCAAGTTTATTTCATACAAAA
1 TTCAAATTAACATAGAAATGAAAATGCAAATGGAAACAATTAAATCAAGTTTATTTCATACAAAA
38051 TTTCATGTCATTCATCTCAACTAC
66 TTTCATGTCATTCATCTCAACTAC
38075 TTCAAATT
1 TTCAAATT
38083 TTAAGTAGCA
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
88 14 0.15
89 80 0.85
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.33
Consensus pattern (89 bp):
TTCAAATTAACATAGAAATGAAAATGCAAATGGAAACAATTAAATCAAGTTTATTTCATACAAAA
TTTCATGTCATTCATCTCAACTAC
Found at i:47192 original size:26 final size:26
Alignment explanation
Indices: 47170--47348 Score: 121
Period size: 26 Copynumber: 6.9 Consensus size: 26
47160 AGCGTAAATT
*
47170 TATATTCATGCTGACGAACGTAAACA
1 TATATTCATGCTGACGAACGTAAACG
* * *
47196 TATATCCATGCTGACGAGCGTACACG
1 TATATTCATGCTGACGAACGTAAACG
* *
47222 TACATTCATGTTGACGAGA-GTAAACG
1 TATATTCATGCTGACGA-ACGTAAACG
* * * *
47248 TATATCCATGCTCACGAGCAT-AACTG
1 TATATTCATGCTGACGAACGTAAAC-G
* * *
47274 TATATTCATGCTGGC-AAGCATAAATG
1 TATATTCATGCTGACGAA-CGTAAACG
* * **
47300 CATAATCATGCTGACGAGTGTAAACG
1 TATATTCATGCTGACGAACGTAAACG
* * * *
47326 TGTAATCATGTTGGCGAACGTAA
1 TATATTCATGCTGACGAACGTAA
47349 TTGCATGTTA
Statistics
Matches: 114, Mismatches: 33, Indels: 12
0.72 0.21 0.08
Matches are distributed among these distances:
25 4 0.04
26 107 0.94
27 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (26 bp):
TATATTCATGCTGACGAACGTAAACG
Found at i:47238 original size:52 final size:51
Alignment explanation
Indices: 47170--47348 Score: 159
Period size: 52 Copynumber: 3.5 Consensus size: 51
47160 AGCGTAAATT
47170 TATATTCATGCTGACGAACGTAAACATATATCCATGCTGACGAGCGTACACG
1 TATATTCATGCTGACGAACGTAAACATATATCCATGCTGACGAGCGTA-ACG
* * * * *
47222 TACATTCATGTTGACGAGA-GTAAACGTATATCCATGCTCACGAGCATAACTG
1 TATATTCATGCTGACGA-ACGTAAACATATATCCATGCTGACGAGCGTAAC-G
* * *
47274 TATATTCATGCTGGC-AAGCATAAATGCATA-AT-CATGCTGACGAGTGTAAACG
1 TATATTCATGCTGACGAA-CGTAAA--CATATATCCATGCTGACGAGCGT-AACG
* * * *
47326 TGTAATCATGTTGGCGAACGTAA
1 TATATTCATGCTGACGAACGTAA
47349 TTGCATGTTA
Statistics
Matches: 102, Mismatches: 17, Indels: 16
0.76 0.13 0.12
Matches are distributed among these distances:
50 1 0.01
51 3 0.03
52 87 0.85
53 8 0.08
54 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (51 bp):
TATATTCATGCTGACGAACGTAAACATATATCCATGCTGACGAGCGTAACG
Found at i:51803 original size:43 final size:43
Alignment explanation
Indices: 51742--51828 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
51732 AATGCTCGCT
*
51742 TATCAACGGGAAGTGATGGTTACATAGATACTGAGTTAAGAGC
1 TATCAACGGGAAGTGATGGTTACATAAATACTGAGTTAAGAGC
* *
51785 TATCAACGGGAAGTGATGGTTGCATAAATGCTGAGTTAAGAGC
1 TATCAACGGGAAGTGATGGTTACATAAATACTGAGTTAAGAGC
51828 T
1 T
51829 TGACCATTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.26
Consensus pattern (43 bp):
TATCAACGGGAAGTGATGGTTACATAAATACTGAGTTAAGAGC
Found at i:54478 original size:26 final size:26
Alignment explanation
Indices: 54444--54659 Score: 234
Period size: 26 Copynumber: 8.3 Consensus size: 26
54434 AGTGTAAATG
54444 TATTCATGCTGACGAGCGTAAACGTA
1 TATTCATGCTGACGAGCGTAAACGTA
*
54470 TATTCATGCTAACGAGCGTAAACGTA
1 TATTCATGCTGACGAGCGTAAACGTA
* * *
54496 CATACATGCTGACGAGCGTAAATGTA
1 TATTCATGCTGACGAGCGTAAACGTA
* *
54522 CATACATGCTGACGAGCGTAAACGTA
1 TATTCATGCTGACGAGCGTAAACGTA
* * *
54548 TATCCATGCTGACGAGTGTAAACATA
1 TATTCATGCTGACGAGCGTAAACGTA
* * *
54574 TATTCATGTTGGCGAGCGTAAATGTA
1 TATTCATGCTGACGAGCGTAAACGTA
* * * * * * *
54600 TACTCATGTTGTCAAGCATAAATGCA
1 TATTCATGCTGACGAGCGTAAACGTA
* *
54626 TAATCATGCTGACGAACGTAAACGTA
1 TATTCATGCTGACGAGCGTAAACGTA
*
54652 TAATCATG
1 TATTCATG
54660 TTGGCGAACG
Statistics
Matches: 161, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 161 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (26 bp):
TATTCATGCTGACGAGCGTAAACGTA
Found at i:57111 original size:19 final size:19
Alignment explanation
Indices: 57089--57135 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
57079 AAACATGTTG
* *
57089 ACTTTGATCATTGACTTTT
1 ACTTTGACCATTGACCTTT
*
57108 ACTTTGACCGTTGACCTTT
1 ACTTTGACCATTGACCTTT
57127 -CTTTGACCA
1 ACTTTGACCA
57136 ATCTTATCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (19 bp):
ACTTTGACCATTGACCTTT
Found at i:59001 original size:42 final size:39
Alignment explanation
Indices: 58911--58998 Score: 133
Period size: 39 Copynumber: 2.3 Consensus size: 39
58901 ATCAAAATAG
**
58911 GAAAACTACTCCTATTTGCACTCTACTTCTAATAATATA
1 GAAAACTACTCCTATTCACACTCTACTTCTAATAATATA
*
58950 GAAAACTACTCCTATTCACCCTCTACTTC-ATATAATATA
1 GAAAACTACTCCTATTCACACTCTACTTCTA-ATAATATA
58989 GAAAACTACT
1 GAAAACTACT
58999 ACTAAAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 1 0.02
39 44 0.98
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.33
Consensus pattern (39 bp):
GAAAACTACTCCTATTCACACTCTACTTCTAATAATATA
Found at i:66490 original size:26 final size:26
Alignment explanation
Indices: 66461--66519 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
66451 CATTCCTATC
66461 TTACCCTCAGCAAAATTTTGACGATT
1 TTACCCTCAGCAAAATTTTGACGATT
** ** *
66487 TTACTTTTGGTAAAATTTTGACGATT
1 TTACCCTCAGCAAAATTTTGACGATT
*
66513 TTGCCCT
1 TTACCCT
66520 TAAGAAATTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (26 bp):
TTACCCTCAGCAAAATTTTGACGATT
Found at i:66797 original size:9 final size:10
Alignment explanation
Indices: 66778--66806 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
66768 CATTTATATT
66778 TTTCTATTCA
1 TTTCTATTCA
66788 TTTC-ATTCA
1 TTTCTATTCA
66797 TTTCTATTCA
1 TTTCTATTCA
66807 AATACACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:68568 original size:28 final size:28
Alignment explanation
Indices: 68527--68581 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
68517 GATATCTGAT
* *
68527 TTACTCCTTGTTGACCCAAAGGTCATGC
1 TTACTCCCTATTGACCCAAAGGTCATGC
68555 TTACTCCCTATTGACCCAAAGGTCATG
1 TTACTCCCTATTGACCCAAAGGTCATG
68582 ATGCTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (28 bp):
TTACTCCCTATTGACCCAAAGGTCATGC
Found at i:68603 original size:36 final size:36
Alignment explanation
Indices: 68555--68649 Score: 147
Period size: 36 Copynumber: 2.6 Consensus size: 36
68545 AAGGTCATGC
* *
68555 TTACTCCCTATTGACCCAAAGGTCATGATGCTCATT
1 TTACTCCTTATTGACCCAAAGGTCATAATGCTCATT
*
68591 TTACTCCTTATTGACCCAAAGGTCCTAATGCTCATT
1 TTACTCCTTATTGACCCAAAGGTCATAATGCTCATT
68627 TTACT-CTCTATTGACCCAAAGGT
1 TTACTCCT-TATTGACCCAAAGGT
68650 TATGCCTGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 2 0.04
36 53 0.96
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (36 bp):
TTACTCCTTATTGACCCAAAGGTCATAATGCTCATT
Found at i:69763 original size:20 final size:19
Alignment explanation
Indices: 69723--69764 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
69713 TCTTTTATAA
*
69723 TTAACTTAATTAACCTTAC
1 TTAACTTAATTAACATTAC
69742 TTAAGCTTAATTAA-ATTCAC
1 TTAA-CTTAATTAACATT-AC
69762 TTA
1 TTA
69765 TTACATCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAACTTAATTAACATTAC
Found at i:70540 original size:14 final size:15
Alignment explanation
Indices: 70521--70554 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
70511 ACTAACTTTT
70521 AATTCAATAATT-AA
1 AATTCAATAATTCAA
*
70535 AATTCATTAATTCAA
1 AATTCAATAATTCAA
70550 AATTC
1 AATTC
70555 CATTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTCAATAATTCAA
Found at i:74299 original size:2 final size:2
Alignment explanation
Indices: 74292--74322 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
74282 ATACTATAAA
74292 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 A
74323 CCTCTACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76504 original size:11 final size:11
Alignment explanation
Indices: 76488--76523 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
76478 ACCTACAAGC
76488 AAAAGAAAAAA
1 AAAAGAAAAAA
*
76499 AAAAGAAAAAG
1 AAAAGAAAAAA
76510 AAAAGAAAAGAA
1 AAAAGAAAA-AA
76522 AA
1 AA
76524 GAACAAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 19 0.86
12 3 0.14
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:76507 original size:10 final size:10
Alignment explanation
Indices: 76488--76531 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
76478 ACCTACAAGC
76488 AAAAGAAAAAA
1 AAAAG-AAAAA
76499 AAAAGAAAAA
1 AAAAGAAAAA
*
76509 GAAAAGAAAAG
1 -AAAAGAAAAA
76520 AAAAGAACAAA
1 AAAAGAA-AAA
76531 A
1 A
76532 GTCCCTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 12 0.41
11 17 0.59
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:76524 original size:5 final size:5
Alignment explanation
Indices: 76488--76526 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
76478 ACCTACAAGC
*
76488 AAAAG AAAAAA AAAAG AAAAAG AAAAG AAAAG AAAAG AA
1 AAAAG -AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AA
76527 CAAAAGTCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 21 0.70
6 9 0.30
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:77029 original size:2 final size:2
Alignment explanation
Indices: 77022--77048 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
77012 AACTGCACAT
77022 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
77049 AATCCTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:88754 original size:23 final size:22
Alignment explanation
Indices: 88722--88846 Score: 90
Period size: 23 Copynumber: 5.5 Consensus size: 22
88712 GCTGGGGAAA
88722 CAGTAAGCACACACAGTACAAT
1 CAGTAAGCACACACAGTACAAT
* * *
88744 CCAGTAGGCACACACGGTGCAAT
1 -CAGTAAGCACACACAGTACAAT
* * **
88767 CAGTAAGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGTAC-AAT
* *
88790 CAGTAAGCACACGA-AGTGCGAAA
1 CAGTAAGCACAC-ACAGTAC-AAT
* * *
88813 CAGTAAGCACACAAAGTGCGAAA
1 CAGTAAGCACACACAGTAC-AAT
88836 CAGTAAGCACA
1 CAGTAAGCACA
88847 TGAAGTGCGA
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
22 15 0.17
23 71 0.82
24 1 0.01
ACGTcount: A:0.42, C:0.26, G:0.22, T:0.11
Consensus pattern (22 bp):
CAGTAAGCACACACAGTACAAT
Found at i:88840 original size:46 final size:44
Alignment explanation
Indices: 88694--88866 Score: 150
Period size: 46 Copynumber: 3.7 Consensus size: 44
88684 CGAAGTACTT
* *
88694 AACAGTAAGCACACAAGTGCTGGGGAAACAGTAAGCACACACAGTACA
1 AACAGTAAGCACACAAGTGC----GAAACAGTAAGCACACAAAGTGCA
* * * * * * *
88742 ATCCAGTAGGCACACACGGTGC-AATCAGTAAGCGCACATAGCGCA
1 A-ACAGTAAGCACACA-AGTGCGAAACAGTAAGCACACAAAGTGCA
88787 AATCAGTAAGCACACGAAGTGCGAAACAGTAAGCACACAAAGTGCGA
1 AA-CAGTAAGCACAC-AAGTGCGAAACAGTAAGCACACAAAGTGC-A
* *
88834 AACAGTAAGCACATGAAGTGCGAAACAATAAGC
1 AACAGTAAGCACA-CAAGTGCGAAACAGTAAGC
88867 GCGCTAGCGT
Statistics
Matches: 101, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
45 34 0.34
46 47 0.47
47 3 0.03
48 1 0.01
49 12 0.12
50 4 0.04
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (44 bp):
AACAGTAAGCACACAAGTGCGAAACAGTAAGCACACAAAGTGCA
Found at i:88852 original size:23 final size:23
Alignment explanation
Indices: 88790--88866 Score: 127
Period size: 23 Copynumber: 3.3 Consensus size: 23
88780 TAGCGCAAAT
88790 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
88813 CAGTAAGCACACAAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
88836 CAGTAAGCACATGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
88859 CAATAAGC
1 CAGTAAGC
88867 GCGCTAGCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.10
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:92550 original size:9 final size:9
Alignment explanation
Indices: 92538--92563 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
92528 TAAAGAAATC
92538 TTTTATTTT
1 TTTTATTTT
92547 TTTTATTTT
1 TTTTATTTT
92556 TTTTATTT
1 TTTTATTT
92564 CTTACCTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTATTTT
Found at i:93082 original size:23 final size:23
Alignment explanation
Indices: 93039--93083 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
93029 AGGCAAGAGT
* *
93039 GTGCCACAAGGCAGAGGAAAAGC
1 GTGCCACAAGGCAAAGAAAAAGC
*
93062 GTGCCACAAGGTAAAGAAAAAG
1 GTGCCACAAGGCAAAGAAAAAG
93084 TGTAACACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.18, G:0.31, T:0.07
Consensus pattern (23 bp):
GTGCCACAAGGCAAAGAAAAAGC
Found at i:112448 original size:7 final size:7
Alignment explanation
Indices: 112430--112470 Score: 61
Period size: 6 Copynumber: 6.3 Consensus size: 7
112420 TAGCAATATT
112430 TCTTTT-
1 TCTTTTC
112436 TCTTTTC
1 TCTTTTC
112443 TCTTTTC
1 TCTTTTC
112450 TC-TTTC
1 TCTTTTC
112456 TCTTTTC
1 TCTTTTC
112463 T-TTTTC
1 TCTTTTC
112469 TC
1 TC
112471 ATTCAACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 18 0.56
7 14 0.44
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TCTTTTC
Found at i:112468 original size:13 final size:13
Alignment explanation
Indices: 112428--112470 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
112418 TATAGCAATA
112428 TTTCT-TTTTC-T
1 TTTCTCTTTTCTT
*
112439 TTTCTCTTTTCTC
1 TTTCTCTTTTCTT
112452 TTTCTCTTTTCTT
1 TTTCTCTTTTCTT
112465 TTTCTC
1 TTTCTC
112471 ATTCAACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 5 0.18
12 5 0.18
13 18 0.64
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCTCTTTTCTT
Found at i:134971 original size:679 final size:679
Alignment explanation
Indices: 132733--137391 Score: 4565
Period size: 679 Copynumber: 6.9 Consensus size: 679
132723 AACCAATATT
* * * * * * * *
132733 ATACCATTGTTGGGACCATCAATACGTCCCGTGGCACAGTGGAAAGATTATTCCAAG-AATACTC
1 ATACCATTGTTGGGATCACCAATATGCCCCGTGGCATAGTGAAAAAATTATTCC--GCAATCCTC
* * * * * * *
132797 AACCATGAAT-CATTGTATGAGAAATGAAACT-GTTTGTAATAAGGTTGAAGATATATCTTATTA
64 AGCCATGGATCCA-TGTATGAGGAATGAAA-TGGGTTGAAATAAGGTTGAAGATATACCTTCTTA
* * ** ** * ** ***
132860 ACTAAAAAAAGATGAAAGGATGCTATTGATTCGATGTCGATTCCAAGTCACAACGAAAATGTGTA
127 ACTAAAAAATGCTGAAAGGATTTTGCTGATTCGATGTCGATTCCAAGCCACAACGAAAACATCCC
* * * * * * * * *
132925 GAACTTTACATAGTCCACTCGATATTAAAATGAATGG-AAAAATTTATAAAACTACACTCAGATA
192 GACCTCTACGTAGTCCACTCGATATTAAAACGAATGGTAAAATTTTA-AAAATTGCACTCAAATC
* *
132989 TCTGTGTAAAAACGTCACCCTTTGACAACTTTTATTAAAACAAGATAATACTTTTTTAAAAATTT
256 TCTGTGGAAAAACGTCACCCTTTGACAACTTTTATTAAAACAAGATAATA-TTTTTTTAAAA-TT
* * * *
133054 TTGATCTAAGATGCTTCTTACTGGAACAACTTTTG-TCTTTTTTTGAATGTAACTAACAAGTGAA
319 TCGATCTAAGATGCTTCTTACTGGAACAACTTTTGTTCTTTTTTCGAATGTAACTGACAAGTTAA
** * ** *
133118 CAATTAACTTTTAATGACAAAAA---C--TG-CATAA-ACAA-ATTTGTTAACACTTAACAAACC
384 CAATTAACTTCGAATGATAAAAACCCCATTGCCCCAAGA-AAGATTCGTTAACACTTAACAAACC
* *
133175 ATATACAACATCCAATGGGCTTCAGAATCAATGATTAACACTTAATCATCAATTGATAGGAACAA
448 ATATACAACATCCAATGGGCTTCAGAATCAATGATT-ACACTTAATCATCGATTGAGAGGAACAA
* * * * *
133240 ATACTCGCATAGGTTTAACAGATTAAACATGCACGTTTTAAACAACAATTAATAGATATCATATA
512 ATACTCACATAGGTTTAACAGATTAAACATACACGTTTTAAACAACAGTTAATAAATTTCATATA
*
133305 TTCATAAAAACAGATT-GATTAAACATATCAAATAACATGTATCTCATACAATCGCATCAACCAA
577 TTCATAAAAATAG-TTCGATTAAACATATCAAATAACATGTATCTCATACAATCGCATCAACCAA
* * * * *
133369 TCAATTTAATCTCGAATCTGTATCCAACAAGTGGCTTTT
641 TAAATTTAATCTCGAATCAGTATCCTACAAGGGGCTTTG
* * * * * * * * * *
133408 ATACCATTGCTGGGACCATCAGTATGCCCTGCGACGTAGTG-GAAAATTATTCAGGCAATCCTCA
1 ATACCATTGTTGGGATCACCAATATGCCCCGTGGCATAGTGAAAAAATTATTC-CGCAATCCTCA
* * * * ** * *
133472 GCCATGGATCGATGTACGTGGAATGAAACGGGTTGAAATAAGAATGAGGATATACCTTTTTTAAC
65 GCCATGGATCCATGTATGAGGAATGAAATGGGTTGAAATAAGGTTGAAGATATACC-TTCTTAAC
* ** * ** ** ** *
133537 TGAAAAACACTTAAAGGATGCTGCTGATTCGATGTCGATTCCAAGCCACAAAAAAAATGTCTCGA
129 TAAAAAATGCTGAAAGGATTTTGCTGATTCGATGTCGATTCCAAGCCACAACGAAAACATCCCGA
* ** * * * * *
133602 CCTCTACGTAGTTCACTCGATATTAAAACGAATGAAAAAATTTTAAAAACTGCACTTAGATATAT
194 CCTCTACGTAGTCCACTCGATATTAAAACGAATGGTAAAATTTTAAAAATTGCACTCAAATCTCT
* * ** * * * *
133667 GTGTAAAAATGTCACAGTTTGACAACTTTTATTAAAATAGGTTAATATTTTTTTAAAATTTAGAT
259 GTGGAAAAACGTCACCCTTTGACAACTTTTATTAAAACAAGATAATATTTTTTTAAAATTTCGAT
* * **
133732 CTAAGATGCTTCTTACTAGTAA-AAATTTTGTTCTTTTTTTTAATGTAACT-AGCAAGTTAACAA
324 CTAAGATGCTTCTTACT-GGAACAACTTTTGTTCTTTTTTCGAATGTAACTGA-CAAGTTAACAA
* * * * *
133795 TTAACTTTGAATAATAAAAACCCCA-T------AGACAGATTTGTTAACACTTAACAAATCATAT
387 TTAACTTCGAATGATAAAAACCCCATTGCCCCAAGAAAGATTCGTTAACACTTAACAAACCATAT
* * *
133853 ACAACATCCAATGGGCTTTAGAATCAATGATTGACACTTAATCATCGATTGATAAGAACAAATAC
452 ACAACATCCAATGGGCTTCAGAATCAATGATT-ACACTTAATCATCGATTGAGAGGAACAAATAC
* * * * * * * *
133918 TCACATAGGTTTAACATATTAAACATGCATGTTTTAAAAAACAATTAATAGATATCTTATATTCA
516 TCACATAGGTTTAACAGATTAAACATACACGTTTTAAACAACAGTTAATAAATTTCATATATTCA
* ** * * * *
133983 TAAAAACAAATCAATTAAACATATCAAGTAACATGCATCTCATACAATCGCATCAACCAATCAAT
581 TAAAAATAGTTCGATTAAACATATCAAATAACATGTATCTCATACAATCGCATCAACCAATAAAT
*
134048 TTAATCTCGAAT-ATGTATCCTACAAGTGGCTCTT-
646 TTAATCTCGAATCA-GTATCCTACAAGGGGCT-TTG
* * * * *
134082 ATACCATTGTTTGGA-CAACTAGTATGCCCCGTGGCATAGTGGAAAAATTATTCCAGCAATCCTT
1 ATACCATTGTTGGGATC-ACCAATATGCCCCGTGGCATAGTGAAAAAATTATTCC-GCAATCCTC
* * * * * *
134146 AACCATGGATCTA-GTTACGAGGAATGAAACGGGATGAAATAAGGTTGAAGAAATACCTTCTTAA
64 AGCCATGGATCCATG-TATGAGGAATGAAATGGGTTGAAATAAGGTTGAAGATATACCTTCTTAA
* ** * * * * * * * * *
134210 CTGAAAAACACTGAAAGAATGCTAG-TGATTTGATATCAATTCCAAGCCACAA-TAATAGCGTCC
128 CTAAAAAATGCTGAAAGGAT-TTTGCTGATTCGATGTCGATTCCAAGCCACAACGAA-AACATCC
* ** * * *
134273 CGAGCTCTAAATAGTCCACTTGATATTAAAACGAATGGTAAAATTTTAAAAACTGCACTTAAATC
191 CGACCTCTACGTAGTCCACTCGATATTAAAACGAATGGTAAAATTTTAAAAATTGCACTCAAATC
* * * * ***
134338 TGTGTGGTAAAGCGTTATTGTTTGACAACTTTTATTAAAA-AAGAATAATA-TTTTTT-AAATTT
256 TCTGTGGAAAAACGTCACCCTTTGACAACTTTTATTAAAACAAG-ATAATATTTTTTTAAAATTT
* * * * * * * *
134400 CGATTTCATATGCTTCTTACTGGAACAACTTTTGTTCATTTTTCGATTGTAGCTTACAAGTTAAG
320 CGATCTAAGATGCTTCTTACTGGAACAACTTTTGTTCTTTTTTCGAATGTAACTGACAAGTTAAC
* * * * ***
134465 AATTAACTTCAAATGATAAAGACCCCATTACCTCAAGAAAGATTCGTTAACACTTAACAAATTGT
385 AATTAACTTCGAATGATAAAAACCCCATTGCCCCAAGAAAGATTCGTTAACACTTAACAAACCAT
* * * * * * * * *
134530 ATACACCAT-TATACGGGATTTAGAATTAAAT-ATT-CACTTGATCATCAATTGAGAGGAAAAAA
450 ATACAACATCCA-ATGGGCTTCAGAA-TCAATGATTACACTTAATCATCGATTGAGAGGAACAAA
* *
134592 TACTCACATAGGTTTAACAGATTAAACATACACGTTTTAAACAACAATTAATGAATTTCATATAT
513 TACTCACATAGGTTTAACAGATTAAACATACACGTTTTAAACAACAGTTAATAAATTTCATATAT
* * *
134657 TCATAAAAATAGTTCGATTAAACATATCAAAAAACATGTATCTCATACAATCGCATAAACCCCAC
578 TCATAAAAATAGTTCGATTAAACATATCAAATAACATGTATCTCATACAATCGCATCAA--CCAA
* * ** * *
134722 TAAATTTGATCTTGAATCAGTATTGTATATGGGGCTTTG
641 TAAATTTAATCTCGAATCAGTATCCTACAAGGGGCTTTG
* *** * *** ** *
134761 ATACCATTTTTGGGATTGTCGATATGCTTTGTGGCGCAGTGAAAAAATTATTCACGCGATCCTCA
1 ATACCATTGTTGGGATCACCAATATGCCCCGTGGCATAGTGAAAAAATTATTC-CGCAATCCTCA
* * * * * * *
134826 GCCATCGATCTATGTATGAGGAATGAAATAGGTTGAAATAAGATTAAAGATATAGCTTATTAACT
65 GCCATGGATCCATGTATGAGGAATGAAATGGGTTGAAATAAGGTTGAAGATATACCTTCTTAACT
134891 AAAAAATGCTGAAAGGATTTTGCTGATTCGATGTCGATTCCAAGCCACAACGAAAACATCCCGAC
130 AAAAAATGCTGAAAGGATTTTGCTGATTCGATGTCGATTCCAAGCCACAACGAAAACATCCCGAC
* * * * *
134956 CTCTATGTAGTCCACTAGATATTAAAATGAATGG-AAAATTTTAAAAAATTGCACCCAGATCTCT
195 CTCTACGTAGTCCACTCGATATTAAAACGAATGGTAAAATTTT-AAAAATTGCACTCAAATCTCT
* ** *
135020 GTGGAAAAATGTCACCCTTTGAGGACATTTATTAAAACAAGATAATATTTTTTTAAAAATTTCGA
259 GTGGAAAAACGTCACCCTTTGACAACTTTTATTAAAACAAGATAATATTTTTTT-AAAATTTCGA
* * * *
135085 TCTAAGATGCTTCTTACTAGAACAACTGTTGTTTTTTTTTCGAATGTAACGGACAAGTTAACAAT
323 TCTAAGATGCTTCTTACTGGAACAACTTTTGTTCTTTTTTCGAATGTAACTGACAAGTTAACAAT
* * *
135150 TAACTTCGAATGATAAAAACCCCACTGCCCCAAGATAGATTCGTTAACACTCAA-AAGACCATAT
388 TAACTTCGAATGATAAAAACCCCATTGCCCCAAGAAAGATTCGTTAACACTTAACAA-ACCATAT
*
135214 ACAACATCCAATGGGCTTCAGAATCAATGATTGACACTAAATCATCGATTGAGAGGAACAAATAC
452 ACAACATCCAATGGGCTTCAGAATCAATGATT-ACACTTAATCATCGATTGAGAGGAACAAATAC
* * * *
135279 TAACATAGGTTTAATAGATTAAGCATACACGTTTTAAACAACAGTTAAAAAATTTCATATATTCA
516 TCACATAGGTTTAACAGATTAAACATACACGTTTTAAACAACAGTTAATAAATTTCATATATTCA
* *
135344 CAAAAATAGTTCGATAAAACATATCAAATAACATGTATCTCATACAATCGCATCAACCAATAAAT
581 TAAAAATAGTTCGATTAAACATATCAAATAACATGTATCTCATACAATCGCATCAACCAATAAAT
* ** * * * *
135409 TTAATCTCGAATCCGTATTGTATATGGGGCTCTA
646 TTAATCTCGAATCAGTATCCTACAAGGGGCTTTG
* * * ** *
135443 ATACCATTGTTGGGATTACCAATATGCCCCGTGACATAGTGAAAAAATTATTCTAGTGATCCTTA
1 ATACCATTGTTGGGATCACCAATATGCCCCGTGGCATAGTGAAAAAATTATTC-CGCAATCCTCA
* * * * *
135508 GCTATCGATCCATGTATGAGGAACGAAACGTGTTGAAATAAGGTTGAAGATATACCTTCTTAAC-
65 GCCATGGATCCATGTATGAGGAATGAAATGGGTTGAAATAAGGTTGAAGATATACCTTCTTAACT
* * * * *
135572 AAAAAATGCTAAAAGGATGTTT-CTGATTCGTTGTCAATTCCAAGCCACAATGAAAACATCCTGA
130 AAAAAATGCTGAAAGGAT-TTTGCTGATTCGATGTCGATTCCAAGCCACAACGAAAACATCCCGA
* * * *
135636 CCTCTATGTAGTCTAC-CAGATATTAAAATGAATGGT-AAATTTTAAAAAATTGCACCCAAATCT
194 CCTCTACGTAGTCCACTC-GATATTAAAACGAATGGTAAAATTTT-AAAAATTGCACTCAAATCT
* *
135699 CTGTGGAAAAATGTCACCCTTTGACAACTTTTATTAAAACATGATAATATTTTTTTAAAATTTCG
257 CTGTGGAAAAACGTCACCCTTTGACAACTTTTATTAAAACAAGATAATATTTTTTTAAAATTTCG
* * * * *
135764 ATCTAAGATGATTCTTACTAGAACAAATTTTGTTCTTTTTTCGATTGTAACTGACAAGTTAAAAA
322 ATCTAAGATGCTTCTTACTGGAACAACTTTTGTTCTTTTTTCGAATGTAACTGACAAGTTAACAA
*** * * * * *
135829 TTAACTTCGAATGATAAAAACATTATTGCCCC-AGACATATTCCTTAACGCTTAACAGACCATAT
387 TTAACTTCGAATGATAAAAACCCCATTGCCCCAAGAAAGATTCGTTAACACTTAACAAACCATAT
* * *
135893 ACAACATCCAATGGGCTTCAAAATCAATGATTAACACTTAATCATTGATTGAGAGGAATAAATAC
452 ACAACATCCAATGGGCTTCAGAATCAATGATT-ACACTTAATCATCGATTGAGAGGAACAAATAC
* * *
135958 TCACATAGGTTTAACAGATTAAACATGCATGTTTTAAA-ATCCAGTTAATAGATATTT--TATAT
516 TCACATAGGTTTAACAGATTAAACATACACGTTTTAAACA-ACAGTTAATA-A-ATTTCATATAT
* * * * ** ** *
136020 TCATAAAAATAGATCGATTAAACATATCAATTAAAATATATCTCATATGATTACATCAACCAATC
578 TCATAAAAATAGTTCGATTAAACATATCAAATAACATGTATCTCATACAATCGCATCAACCAATA
** * * * *
136085 AATTTAATCTCGAATCCCTATCCTACACGTGTCTTTT
643 AATTTAATCTCGAATCAGTATCCTACAAGGGGCTTTG
* * * * * **
136122 ATACCATTTTTTGGACCACCAATATGACCCCGTGGCATAGCGAAAAATTTATTCCAATAATCCTC
1 ATACCATTGTTGGGATCACCAATATG-CCCCGTGGCATAGTGAAAAAATTATTCC-GCAATCCTC
* * * * *
136187 AGCCATGGATCCATGTAGGAGGAA-CAACACGAGTTGAAATAAGGTTGAAGAAATACCTTCTTAA
64 AGCCATGGATCCATGTATGAGGAATGAA-ATGGGTTGAAATAAGGTTGAAGATATACCTTCTTAA
** * * ** * * * *
136251 CTAAAAAAAACTAAAAGAATGTAAG-TGATTTGATATCGACTCCAAGCCACAACGATAACATCCC
128 CTAAAAAATGCTGAAAGGAT-TTTGCTGATTCGATGTCGATTCCAAGCCACAACGAAAACATCCC
* ** * * * ** *
136315 GAGCTCTATATAGTCCACTTGATATTAAAACGAATGGTAAAATTTAAAAAATTACACTCTGATAT
192 GACCTCTACGTAGTCCACTCGATATTAAAACGAATGGTAAAATTTTAAAAATTGCACTCAAATCT
* * * * *
136380 TTGGGGAAAAGCGTCACTACTGTTTGACAACTTTTATTAAAA-TAGAGTAATATTTTTTTAAAAT
257 CTGTGGAAAAACGTCAC--C-CTTTGACAACTTTTATTAAAACAAGA-TAATATTTTTTTAAAAT
* * * * * * * *
136444 TTTGATCTAAGATGCTTCCTACTGAAACAAATTTTGTTCATTTTTCAAATGTAACTTAAAAGTTA
318 TTCGATCTAAGATGCTTCTTACTGGAACAACTTTTGTTCTTTTTTCGAATGTAACTGACAAGTTA
* * *
136509 ACAATTAACTTCGAATAATAAAAACCCCATTGCCCCAAGAAAGATTCATTAACACTTAACAAGCC
383 ACAATTAACTTCGAATGATAAAAACCCCATTGCCCCAAGAAAGATTCGTTAACACTTAACAAACC
* * * *
136574 ATATACAACATTCAATGGGCTTTAGAATTAAAT-ATTCACACTTAATCTTCGATTGAGAGGAACA
448 ATATACAACATCCAATGGGCTTCAGAA-TCAATGATT-ACACTTAATCATCGATTGAGAGGAACA
* ** *
136638 AATACTCACATAGGTTTAACAGATTAAACATACACATTTTAAACAGTAGTTAAAAAATTTCATAT
511 AATACTCACATAGGTTTAACAGATTAAACATACACGTTTTAAACAACAGTTAATAAATTTCATAT
* * * *
136703 ATTCATAAAAATAGTTCAATTAAACATATGAAATAACATGTATCTCATACAATCACATCAACAAA
576 ATTCATAAAAATAGTTCGATTAAACATATCAAATAACATGTATCTCATACAATCGCATCAACCAA
* * * * * *
136768 TAAATTTAATCTAGAATCTGTATCGTATAAGGGACTCTG
641 TAAATTTAATCTCGAATCAGTATCCTACAAGGGGCTTTG
* * * *** * *
136807 ATACCACTGTTGGGAT-AGCCGATATGCCCTGTGGTGCAGTAGAAAAAGTT-TTCCGACGATCCT
1 ATACCATTGTTGGGATCA-CCAATATGCCCCGTGGCATAGT-GAAAAAATTATTCCG-CAATCCT
* * *
136870 CCA-CCATGGATCCATGTATGAGGAATGAAATGGGTTAAAATAAGGTTAAAGATATACCTTCTCA
63 -CAGCCATGGATCCATGTATGAGGAATGAAATGGGTTGAAATAAGGTTGAAGATATACCTTCTTA
* * * * * * * * *
136934 ACTAAAAAATGCTTAAAGAATATTGTTTATTCGATGTCGATTCCAAGTCACAACAAAAATATCCT
127 ACTAAAAAATGCTGAAAGGATTTTGCTGATTCGATGTCGATTCCAAGCCACAACGAAAACATCCC
* * * * * *
136999 GACCTCGACGTAGTCTACCCGATATTAAAACAAATTGTAAAA-TTTAAAAATTGCACCCAAATCT
192 GACCTCTACGTAGTCCACTCGATATTAAAACGAATGGTAAAATTTTAAAAATTGCACTCAAATCT
* * * ** * *
137063 TTGTTGAAAAACGTCGCTATTTGACGAA-ATTTATTAAAACAAGATAATATTTTTTTAAAATTTT
257 CTGTGGAAAAACGTCACCCTTTGAC-AACTTTTATTAAAACAAGATAATATTTTTTTAAAATTTC
* * * * ** * *
137127 GATTTAAGATGCCTCTTACTGGAACAACTTTTGCTGTTTTTTTTAATGTAACTGAAAAGGTAACA
321 GATCTAAGATGCTTCTTACTGGAACAACTTTTGTTCTTTTTTCGAATGTAACTGACAAGTTAACA
* * *
137192 ATTGAA-TTCGAATGAT-AAAACCCCATTGCCCCAAGAAA-ATTTTGTTAACACTTAATAGACCA
386 ATT-AACTTCGAATGATAAAAACCCCATTGCCCCAAGAAAGA-TTCGTTAACACTTAACAAACCA
*
137254 TATACAACATCCAATGGGCTTCATAATCAATGATTAACACTTAATCATCGATTGAGAGGAACAAA
449 TATACAACATCCAATGGGCTTCAGAATCAATGATT-ACACTTAATCATCGATTGAGAGGAACAAA
* * * * * *
137319 TACTCACATAGGTTTAACATATTAAACATACACCTTTTAAACAGCAGTTAACAAATATCTTATAT
513 TACTCACATAGGTTTAACAGATTAAACATACACGTTTTAAACAACAGTTAATAAATTTCATATAT
137384 TCATAAAA
578 TCATAAAA
137392 TCAAATTGAT
Statistics
Matches: 3321, Mismatches: 574, Indels: 174
0.82 0.14 0.04
Matches are distributed among these distances:
671 3 0.00
672 76 0.02
673 48 0.01
674 524 0.16
675 248 0.07
676 8 0.00
677 132 0.04
678 20 0.01
679 696 0.21
680 302 0.09
681 289 0.09
682 283 0.09
683 38 0.01
684 412 0.12
685 237 0.07
686 5 0.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (679 bp):
ATACCATTGTTGGGATCACCAATATGCCCCGTGGCATAGTGAAAAAATTATTCCGCAATCCTCAG
CCATGGATCCATGTATGAGGAATGAAATGGGTTGAAATAAGGTTGAAGATATACCTTCTTAACTA
AAAAATGCTGAAAGGATTTTGCTGATTCGATGTCGATTCCAAGCCACAACGAAAACATCCCGACC
TCTACGTAGTCCACTCGATATTAAAACGAATGGTAAAATTTTAAAAATTGCACTCAAATCTCTGT
GGAAAAACGTCACCCTTTGACAACTTTTATTAAAACAAGATAATATTTTTTTAAAATTTCGATCT
AAGATGCTTCTTACTGGAACAACTTTTGTTCTTTTTTCGAATGTAACTGACAAGTTAACAATTAA
CTTCGAATGATAAAAACCCCATTGCCCCAAGAAAGATTCGTTAACACTTAACAAACCATATACAA
CATCCAATGGGCTTCAGAATCAATGATTACACTTAATCATCGATTGAGAGGAACAAATACTCACA
TAGGTTTAACAGATTAAACATACACGTTTTAAACAACAGTTAATAAATTTCATATATTCATAAAA
ATAGTTCGATTAAACATATCAAATAACATGTATCTCATACAATCGCATCAACCAATAAATTTAAT
CTCGAATCAGTATCCTACAAGGGGCTTTG
Found at i:139550 original size:17 final size:17
Alignment explanation
Indices: 139528--139561 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
139518 CACTAACACT
139528 AAAATGCAACGACAATG
1 AAAATGCAACGACAATG
139545 AAAATGCAACGACAATG
1 AAAATGCAACGACAATG
139562 CTTACTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.18, T:0.12
Consensus pattern (17 bp):
AAAATGCAACGACAATG
Found at i:146695 original size:15 final size:16
Alignment explanation
Indices: 146661--146697 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
146651 TTTTACATGC
*
146661 CCTTTTGAAACTTATG
1 CCTTTTGAAACGTATG
146677 -CTTTT-AAACGTATG
1 CCTTTTGAAACGTATG
146691 CCTTTTG
1 CCTTTTG
146698 GACTTTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.46
Consensus pattern (16 bp):
CCTTTTGAAACGTATG
Found at i:150312 original size:17 final size:17
Alignment explanation
Indices: 150292--150329 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
150282 TTATTTACCA
150292 TTTAAGACAATTTTTA-T
1 TTTAA-ACAATTTTTAGT
*
150309 TTTAAATAATTTTTAGT
1 TTTAAACAATTTTTAGT
150326 TTTA
1 TTTA
150330 TTCTTAGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTAAACAATTTTTAGT
Found at i:153354 original size:31 final size:31
Alignment explanation
Indices: 153316--153374 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
153306 GAACTTTTTG
153316 ATACTTTATGAAAAGTATTAATACCAGATCA
1 ATACTTTATGAAAAGTATTAATACCAGATCA
*
153347 ATACTTTATGAAAAGTATTGATACCAGA
1 ATACTTTATGAAAAGTATTAATACCAGA
153375 CCGATACCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (31 bp):
ATACTTTATGAAAAGTATTAATACCAGATCA
Found at i:156482 original size:31 final size:31
Alignment explanation
Indices: 156435--156502 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
156425 AGGTAATTTT
*
156435 TTGATACTTTACGAAAAGCATCGATACTAAA
1 TTGATAATTTACGAAAAGCATCGATACTAAA
* ** *
156466 TTGATAATTTATGAAAATTATCGATACTAGA
1 TTGATAATTTACGAAAAGCATCGATACTAAA
156497 TTGATA
1 TTGATA
156503 CCAAATCGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (31 bp):
TTGATAATTTACGAAAAGCATCGATACTAAA
Found at i:159627 original size:51 final size:51
Alignment explanation
Indices: 159559--159750 Score: 251
Period size: 51 Copynumber: 3.8 Consensus size: 51
159549 CCATATAGGA
* ** * * * *
159559 ATTCATATACTCACGATGACACAAAGTCATTGGACCCTTAATCCATCATGG
1 ATTCATTTACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGG
* ** *
159610 ATCCATTTACTCACGATGACACTTAGTCATCAGACCTTTAATTCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGG
159661 ATTCATTTACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGG
* *
159712 ATTCATTTACTCACGATGATACGTAGTC-TTCGGACCTTT
1 ATTCATTTACTCACGATGACACTTAGTCATT-GGACCTTT
159751 TCGTTTATAG
Statistics
Matches: 123, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
50 2 0.02
51 121 0.98
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGG
Found at i:159691 original size:102 final size:103
Alignment explanation
Indices: 159513--159750 Score: 284
Period size: 102 Copynumber: 2.3 Consensus size: 103
159503 TTTCATTTAA
* * *
159513 TACTCACGTTGACA-TATAGTCATCAGACCTCTTGTTCCATATAGGAATTCATATACTCACGATG
1 TACTCACGATGACACT-TAGTCATCAGACCT-TTATTCCATAAAGGAATTCATATACTCACGATG
* *
159577 ACACAAAGTCATTGGACCCTTAATCCATCATGGATCCATT
64 ACACAAAGTCATTGGACCCTTAATCCATAAAGGATCCATT
* *
159617 TACTCACGATGACACTTAGTCATCAGACCTTTAATT-CGTAAAGG-ATTCATTTACTCACGATGA
1 TACTCACGATGACACTTAGTCATCAGACCTTT-ATTCCATAAAGGAATTCATATACTCACGATGA
** * * *
159680 CACTTAGTCATTGGACCTTTAATCCGTAAAGGATTCATT
65 CACAAAGTCATTGGACCCTTAATCCATAAAGGATCCATT
* * * *
159719 TACTCACGATGATACGTAGTCTTCGGACCTTT
1 TACTCACGATGACACTTAGTCATCAGACCTTT
159751 TCGTTTATAG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
102 78 0.67
103 8 0.07
104 29 0.25
105 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (103 bp):
TACTCACGATGACACTTAGTCATCAGACCTTTATTCCATAAAGGAATTCATATACTCACGATGAC
ACAAAGTCATTGGACCCTTAATCCATAAAGGATCCATT
Found at i:176844 original size:198 final size:198
Alignment explanation
Indices: 176506--176898 Score: 750
Period size: 198 Copynumber: 2.0 Consensus size: 198
176496 TCCTGAGAAA
176506 AATACATTGGCAAGGTCAAGGCTCCAATGGATCCTCAGCCCAATGAGGAGGATGAATATTGAACT
1 AATACATTGGCAAGGTCAAGGCTCCAATGGATCCTCAGCCCAATGAGGAGGATGAATATTGAACT
176571 TTAATATTTTTAAGACGTTGATTTTAAGACTTGTAGTTTTTGGATAATTTTTTAATTTTTAGGGA
66 TTAATATTTTTAAGACGTTGATTTTAAGACTTGTAGTTTTTGGATAATTTTTTAATTTTTAGGGA
* *
176636 CTTATATAATTCGTAGGAGTAGGATTAGGAATTATATTTTTATGCTTTAGATCTTTTGTAGGAAC
131 CTTATATAATTCGTAGGAGTAGGATTAGGAATTATATTTGTATGCTTCAGATCTTTTGTAGGAAC
176701 CTC
196 CTC
176704 AATACATTGGCAAGGTCAAGGCTCCAATGGATCCTCAGCCCAATGAGGAGGATGAATATTGAACT
1 AATACATTGGCAAGGTCAAGGCTCCAATGGATCCTCAGCCCAATGAGGAGGATGAATATTGAACT
* *
176769 TTAATTTTTTTAAGACGTTGATTTTAAGACTTGTAGTTTTTGGATAATTTTTTAATTTTTAGTGA
66 TTAATATTTTTAAGACGTTGATTTTAAGACTTGTAGTTTTTGGATAATTTTTTAATTTTTAGGGA
176834 CTTATATAATTCGTAGGAGTAGGATTAGGAATTATATTTGTATGCTTCAGATCTTTTGTAGGAAC
131 CTTATATAATTCGTAGGAGTAGGATTAGGAATTATATTTGTATGCTTCAGATCTTTTGTAGGAAC
176899 ATCATATTTT
Statistics
Matches: 191, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
198 191 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (198 bp):
AATACATTGGCAAGGTCAAGGCTCCAATGGATCCTCAGCCCAATGAGGAGGATGAATATTGAACT
TTAATATTTTTAAGACGTTGATTTTAAGACTTGTAGTTTTTGGATAATTTTTTAATTTTTAGGGA
CTTATATAATTCGTAGGAGTAGGATTAGGAATTATATTTGTATGCTTCAGATCTTTTGTAGGAAC
CTC
Found at i:177630 original size:21 final size:21
Alignment explanation
Indices: 177606--177645 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
177596 AAGTGAAAAG
177606 AACA-AAAAGAAAATGAGTACA
1 AACATAAAAGAAAA-GAGTACA
177627 AACATAAAAGAAAAGAGTA
1 AACATAAAAGAAAAGAGTA
177646 AGAAAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.68, C:0.07, G:0.15, T:0.10
Consensus pattern (21 bp):
AACATAAAAGAAAAGAGTACA
Found at i:181105 original size:13 final size:13
Alignment explanation
Indices: 181079--181111 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
181069 GTAAATATAA
181079 TTTTTTTTCTTCT
1 TTTTTTTTCTTCT
181092 TTTTCTTTTC-TCT
1 TTTT-TTTTCTTCT
181105 TTTTTTT
1 TTTTTTT
181112 CAAGTGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 11 0.58
14 5 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:187823 original size:13 final size:14
Alignment explanation
Indices: 187805--187834 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
187795 GTCAACGCAA
187805 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
187818 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
187832 TCA
1 TCA
187835 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:195374 original size:13 final size:13
Alignment explanation
Indices: 195356--195380 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
195346 CCCATTTTAT
195356 CATTTTTAGCATG
1 CATTTTTAGCATG
195369 CATTTTTAGCAT
1 CATTTTTAGCAT
195381 TTTTAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:209482 original size:36 final size:36
Alignment explanation
Indices: 209442--209515 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
209432 AAGTGCTCCA
209442 AGGACAAAAAGAGTTAGTTTTTTATTTTCAGCACAT
1 AGGACAAAAAGAGTTAGTTTTTTATTTTCAGCACAT
209478 AGGACAAAAAGAGTTAGTTTTTTATTTTCAGCACAT
1 AGGACAAAAAGAGTTAGTTTTTTATTTTCAGCACAT
209514 AG
1 AG
209516 TTTACTTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (36 bp):
AGGACAAAAAGAGTTAGTTTTTTATTTTCAGCACAT
Found at i:219867 original size:16 final size:17
Alignment explanation
Indices: 219813--219884 Score: 92
Period size: 17 Copynumber: 4.3 Consensus size: 17
219803 ATTGTCCTTA
*
219813 CATTTTTATTGTTACTG
1 CATTTTTATTGTCACTG
*
219830 CATTTTTATTGTCACTA
1 CATTTTTATTGTCACTG
*
219847 TATTTTT-TTGTCACTG
1 CATTTTTATTGTCACTG
* *
219863 CATTTTTATTATCATTG
1 CATTTTTATTGTCACTG
219880 CATTT
1 CATTT
219885 CCATATATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.30
17 33 0.70
ACGTcount: A:0.19, C:0.14, G:0.08, T:0.58
Consensus pattern (17 bp):
CATTTTTATTGTCACTG
Found at i:220920 original size:10 final size:10
Alignment explanation
Indices: 220905--220940 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
220895 AAGCTTGGCC
220905 TAATTTTATT
1 TAATTTTATT
220915 TAATTTTA--
1 TAATTTTATT
220923 T-ATTTTATT
1 TAATTTTATT
220932 TAATTTTAT
1 TAATTTTAT
220941 CATGTTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
7 6 0.26
8 1 0.04
9 1 0.04
10 15 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TAATTTTATT
Found at i:220929 original size:17 final size:17
Alignment explanation
Indices: 220907--220940 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
220897 GCTTGGCCTA
220907 ATTTTATTTAATTTTAT
1 ATTTTATTTAATTTTAT
220924 ATTTTATTTAATTTTAT
1 ATTTTATTTAATTTTAT
220941 CATGTTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTATTTAATTTTAT
Found at i:229901 original size:21 final size:21
Alignment explanation
Indices: 229877--229918 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
229867 CTAAATTTGG
229877 AATAAATAA-ATAATATAATAT
1 AATAAATAATA-AATATAATAT
**
229898 AATACCTAATAAATATAATAT
1 AATAAATAATAAATATAATAT
229919 TGGGATCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAAATAATAAATATAATAT
Found at i:236391 original size:92 final size:91
Alignment explanation
Indices: 236234--236416 Score: 348
Period size: 92 Copynumber: 2.0 Consensus size: 91
236224 TGATTCTCAG
236234 ACCCTTTCCTATCTCTGATTTCAACGTCAAATTTTTTATCCATCTGATGAGTCTAGATTTGGTGT
1 ACCCTTTCCTATCTCTGATTTCAACGTCAAATTTTTTATCCATCTGATGAGTCTAGATTTGGTGT
236299 CTTTTTTGTTGAAAAGGTATCTCAAC
66 CTTTTTTGTTGAAAAGGTATCTCAAC
*
236325 NACCCTTTCCTATCTCTGATTTCAACGTCAAATTTTTTATCCATCTGATGAGTCTATATTTGGTG
1 -ACCCTTTCCTATCTCTGATTTCAACGTCAAATTTTTTATCCATCTGATGAGTCTAGATTTGGTG
236390 TCTTTTTTGTTGAAAAGGTATCTCAAC
65 TCTTTTTTGTTGAAAAGGTATCTCAAC
236417 GTTGAGTGGT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (91 bp):
ACCCTTTCCTATCTCTGATTTCAACGTCAAATTTTTTATCCATCTGATGAGTCTAGATTTGGTGT
CTTTTTTGTTGAAAAGGTATCTCAAC
Found at i:244732 original size:27 final size:27
Alignment explanation
Indices: 244702--244808 Score: 135
Period size: 27 Copynumber: 4.0 Consensus size: 27
244692 TCACTATCAC
244702 TATCTCCCTCTAGAACAGCTTCCTCCT
1 TATCTCCCTCTAGAACAGCTTCCTCCT
* * *
244729 TATCTCCCTCTAGAATAGCTCCCTCTT
1 TATCTCCCTCTAGAACAGCTTCCTCCT
* *
244756 TATCTCCCTCTGGAATAGCTTCCT-CT
1 TATCTCCCTCTAGAACAGCTTCCTCCT
* *
244782 CTATCTCCCTCTGGAACAACTTCCTCC
1 -TATCTCCCTCTAGAACAGCTTCCTCC
244809 CCTCCCTGTC
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
26 1 0.01
27 68 0.97
28 1 0.01
ACGTcount: A:0.18, C:0.39, G:0.08, T:0.35
Consensus pattern (27 bp):
TATCTCCCTCTAGAACAGCTTCCTCCT
Found at i:246249 original size:27 final size:27
Alignment explanation
Indices: 246184--246239 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
246174 TTTTAAAATC
*
246184 TCAATTTTTTTTAAACCTTTTCTTATT
1 TCAAATTTTTTTAAACCTTTTCTTATT
*
246211 TCAAAATTTTTTAAA-CTTTCTCTTATT
1 TCAAATTTTTTTAAACCTTT-TCTTATT
246238 TC
1 TC
246240 TTCTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (27 bp):
TCAAATTTTTTTAAACCTTTTCTTATT
Found at i:251949 original size:22 final size:24
Alignment explanation
Indices: 251919--251968 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
251909 TCAAACTATT
*
251919 AATTAATTTATTT-TATTTAATTA-
1 AATTAATTT-TTTCTACTTAATTAC
251942 AATT-ATTTTTTCTACTTAATTAC
1 AATTAATTTTTTCTACTTAATTAC
251965 AATT
1 AATT
251969 CCATTAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 3 0.12
22 13 0.54
23 8 0.33
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (24 bp):
AATTAATTTTTTCTACTTAATTAC
Done.