Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008913.1 Hibiscus syriacus cultivar Beakdansim tig00112216_pilon, 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: 629305
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:155112 original size:98 final size:98
Alignment explanation
Indices: 154943--155139 Score: 304
Period size: 98 Copynumber: 2.0 Consensus size: 98
154933 TAATTTTGAT
* *
154943 ATGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTGGTTAACAAATAACCATTCTCGCCTTG
1 ATGCCTTTGAACTGAGTGTAATCGAACTCAAAGGTCTTGGTGAACAAATAACCATTCTCGCCTTG
* *
155008 AGTTATGCTGTCAATAGTTCCTTTAAGTGAAAA
66 ACTTATGCTGCCAATAGTTCCTTTAAGTGAAAA
** * * *
155041 ATGCCTTTGAACTGAGTGTAATCGAACTCGTAGGTCTTGGTGGACATATAACCCTTCTCGCCTTG
1 ATGCCTTTGAACTGAGTGTAATCGAACTCAAAGGTCTTGGTGAACAAATAACCATTCTCGCCTTG
*
155106 ACTTATGTTGCCAATAGTTCCTTTAAGTGAAAA
66 ACTTATGCTGCCAATAGTTCCTTTAAGTGAAAA
155139 A
1 A
155140 ATAGCTCCCC
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (98 bp):
ATGCCTTTGAACTGAGTGTAATCGAACTCAAAGGTCTTGGTGAACAAATAACCATTCTCGCCTTG
ACTTATGCTGCCAATAGTTCCTTTAAGTGAAAA
Found at i:156528 original size:95 final size:95
Alignment explanation
Indices: 156333--156591 Score: 376
Period size: 95 Copynumber: 2.7 Consensus size: 95
156323 AGTTGGATCA
* * * *
156333 ATAAAGCTGGGGTGTTTAACCAATTGCTCTAGAGGGACAGCTCAATATCATTGTATAG-ATATTA
1 ATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTC-A-AGC-TT-TATTGTATATTA
* *
156397 TAATCACTTTTATCAGGCTAGCTGAATATTATCC
62 TAATCACCTTTATCAGGCAAGCTGAATATTATCC
*
156431 ATAAAGCTGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
1 ATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
*
156496 CACCTTTATCAGGCAAGCTGAATCTTATCC
66 CACCTTTATCAGGCAAGCTGAATATTATCC
* *
156526 ATAAAGCTGGGGCATTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATATATAA
1 ATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-TATAA
156591 T
65 T
156592 TTTATAATAT
Statistics
Matches: 148, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
94 4 0.03
95 95 0.64
96 8 0.05
97 1 0.01
98 40 0.27
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (95 bp):
ATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
CACCTTTATCAGGCAAGCTGAATATTATCC
Found at i:166710 original size:4 final size:4
Alignment explanation
Indices: 166687--166740 Score: 63
Period size: 4 Copynumber: 12.5 Consensus size: 4
166677 TTACGAAAAC
*
166687 AAAT AAAAT AAAGA AAAT AAAT AAAAT AAAT AAAT AAAT AAAT AAAT AATAT
1 AAAT -AAAT AAA-T AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AA-AT
166739 AA
1 AA
166741 TAATAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
4 29 0.66
5 15 0.34
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:166717 original size:9 final size:9
Alignment explanation
Indices: 166682--166749 Score: 79
Period size: 9 Copynumber: 7.8 Consensus size: 9
166672 CTAAATTACG
*
166682 AAAACAAAT
1 AAAATAAAT
*
166691 AAAATAAAG
1 AAAATAAAT
166700 AAAATAAAT
1 AAAATAAAT
166709 AAAATAAAT
1 AAAATAAAT
166718 -AAATAAAT
1 AAAATAAAT
166726 -AAATAAAT
1 AAAATAAAT
*
166734 AATAT-AAT
1 AAAATAAAT
166742 AATAATAA
1 AA-AATAA
166750 TGAAAAATGA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
8 21 0.41
9 29 0.57
10 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (9 bp):
AAAATAAAT
Found at i:166742 original size:12 final size:13
Alignment explanation
Indices: 166701--166748 Score: 66
Period size: 12 Copynumber: 3.9 Consensus size: 13
166691 AAAATAAAGA
*
166701 AAATAAATAAAAT
1 AAATAAATAATAT
166714 AAATAAATAA-AT
1 AAATAAATAATAT
166726 AAATAAATAATAT
1 AAATAAATAATAT
166739 -AAT-AATAATA
1 AAATAAATAATA
166749 ATGAAAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 7 0.21
12 15 0.44
13 12 0.35
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATAAATAATAT
Found at i:166960 original size:2 final size:2
Alignment explanation
Indices: 166953--167006 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
166943 AAATGTGAGG
166953 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
166995 TA TA TA TA TA TA
1 TA TA TA TA TA TA
167007 ATAGTATTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:167197 original size:15 final size:15
Alignment explanation
Indices: 167177--167226 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
167167 AAAATAAATA
*
167177 ATAAAATATATACAT
1 ATAAAATATATACGT
167192 ATAAAATAT-TA-GT
1 ATAAAATATATACGT
167205 ATAATATATATATACGT
1 ATAA-A-ATATATACGT
167222 ATAAA
1 ATAAA
167227 TAAAATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.17
14 3 0.10
15 13 0.43
16 3 0.10
17 6 0.20
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (15 bp):
ATAAAATATATACGT
Found at i:169479 original size:65 final size:64
Alignment explanation
Indices: 169346--169553 Score: 192
Period size: 65 Copynumber: 3.2 Consensus size: 64
169336 TGCACTAAGA
* * *
169346 GTGCATCGATGCATGAAATGCATTCAACGTTTCAAAATATCCATAGTGCATCAATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATATCCATAGTGCATCAATGCATAGCTG
* *
169410 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTC-TGAGTGCATCGATGCATAG
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCA-AAATATC-CAT-AGTGCATCAATGCATAG
*
169472 -TAT
62 CT-G
* * ** * * * *
169475 GTGCATTGATGCATGAAATGCATTCGATG-ATCAACTTATTCCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATA-TCCATAGTGCATCAATGCATAG-CT
169539 G
64 G
169540 GTGCATCGATGCAT
1 GTGCATCGATGCAT
169554 CACTTTGAAA
Statistics
Matches: 118, Mismatches: 15, Indels: 21
0.77 0.10 0.14
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 45 0.38
65 64 0.54
66 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATATCCATAGTGCATCAATGCATAGCTG
Found at i:176030 original size:21 final size:21
Alignment explanation
Indices: 176006--176079 Score: 105
Period size: 21 Copynumber: 3.5 Consensus size: 21
175996 ACCATCTCTT
*
176006 TTGGAAATGCGGCAAGTGGTC
1 TTGGAAATGCGGCAAGTGGCC
*
176027 TTGGAAATGCGGTAAGTGGCC
1 TTGGAAATGCGGCAAGTGGCC
*
176048 TTGGAGATGCGGCAAGTGGCC
1 TTGGAAATGCGGCAAGTGGCC
176069 TT-GAGAATGCG
1 TTGGA-AATGCG
176080 CCTGGAGCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 2 0.04
21 45 0.96
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.23
Consensus pattern (21 bp):
TTGGAAATGCGGCAAGTGGCC
Found at i:186505 original size:20 final size:20
Alignment explanation
Indices: 186480--186524 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
186470 ACGAGCGTCA
186480 ATCATCATATCAATACTATC
1 ATCATCATATCAATACTATC
* * *
186500 ATCATCGTATCAATATTATT
1 ATCATCATATCAATACTATC
186520 ATCAT
1 ATCAT
186525 TCTCAATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (20 bp):
ATCATCATATCAATACTATC
Found at i:191372 original size:40 final size:42
Alignment explanation
Indices: 191317--191397 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
191307 AAATGAACAA
* *
191317 CAAATTCGTAACGCGAA-CT-CCAATTTCGCAACACAGTTTC
1 CAAATTCGCAACGCGAATCTCCCAAATTCGCAACACAGTTTC
* *
191357 CAAATTCGCAACGCGAATTTCCCAAATTCGCAACTCAGTTT
1 CAAATTCGCAACGCGAATCTCCCAAATTCGCAACACAGTTT
191398 TTGCAATCGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 16 0.46
41 1 0.03
42 18 0.51
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.26
Consensus pattern (42 bp):
CAAATTCGCAACGCGAATCTCCCAAATTCGCAACACAGTTTC
Found at i:191447 original size:39 final size:40
Alignment explanation
Indices: 191341--191477 Score: 113
Period size: 39 Copynumber: 3.4 Consensus size: 40
191331 GAACTCCAAT
*
191341 TTCGCAACACAG--TTTCCAAATTCGCAACGCGAATTTCCCAAA
1 TTCGCAACACAGAATTTGC-AATTCGCAACGCG-ATTT--CAAA
* **
191383 TTCGCAACTCAGTTTTTGCAA-TCGCAACGCGATTTCAAA
1 TTCGCAACACAGAATTTGCAATTCGCAACGCGATTTCAAA
* * * *
191422 TTCTCAACACGGAATTT-CAATTCGCAACTCGATTTCTGAA
1 TTCGCAACACAGAATTTGCAATTCGCAACGCGATTTC-AAA
*
191462 TTCGCAACGC-GAATTT
1 TTCGCAACACAGAATTT
191478 CTTTTTCGCA
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
38 3 0.04
39 36 0.45
40 10 0.12
41 4 0.05
42 21 0.26
43 2 0.03
44 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (40 bp):
TTCGCAACACAGAATTTGCAATTCGCAACGCGATTTCAAA
Found at i:191449 original size:20 final size:20
Alignment explanation
Indices: 191317--191590 Score: 114
Period size: 20 Copynumber: 13.7 Consensus size: 20
191307 AAATGAACAA
* * * *
191317 CAAATTCGTAACGCGAACTC
1 CAAATTCGCAACACGAATTT
* *
191337 CAATTTCGCAACAC-AGTTT
1 CAAATTCGCAACACGAATTT
*
191356 CCAAATTCGCAACGCGAATTT
1 -CAAATTCGCAACACGAATTT
* **
191377 CCCAAATTCGCAACTCAGTTTTT
1 --CAAATTCGCAACAC-GAATTT
*
191400 GC-AA-TCGCAACGCG-ATTT
1 -CAAATTCGCAACACGAATTT
*
191418 CAAATTCTCAACACGGAATTT
1 CAAATTCGCAACAC-GAATTT
*
191439 C-AATTCGCAACTCG-ATTT
1 CAAATTCGCAACACGAATTT
* *
191457 CTGAATTCGCAACGCGAATTT
1 C-AAATTCGCAACACGAATTT
***
191478 CTTTTTCGCAACAC-AAGTTT
1 CAAATTCGCAACACGAA-TTT
*** * *
191498 CCTTTTCGCAACAAGATTTT
1 CAAATTCGCAACACGAATTT
191518 CTAAA-TCGCAACACGAATTT
1 C-AAATTCGCAACACGAATTT
**** * *
191538 TGTTTTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
**
191558 TGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
* *
191578 TAATTTCGCAACA
1 CAAATTCGCAACA
191591 GCTTTTATTT
Statistics
Matches: 195, Mismatches: 44, Indels: 30
0.72 0.16 0.11
Matches are distributed among these distances:
17 1 0.01
18 10 0.05
19 13 0.07
20 135 0.69
21 17 0.09
22 15 0.08
23 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:191766 original size:14 final size:15
Alignment explanation
Indices: 191747--191784 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
191737 TCCCCATCTC
191747 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
191761 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
191777 TAATTTTT
1 TAATTTTT
191785 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:192445 original size:24 final size:24
Alignment explanation
Indices: 192418--192471 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
192408 GTATTCGAAA
192418 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
192442 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
192466 TTTGAT
1 TTTGAT
192472 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:194760 original size:18 final size:18
Alignment explanation
Indices: 194737--194772 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
194727 AAGCAAAAGG
*
194737 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
194755 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
194773 CAACCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:195054 original size:39 final size:39
Alignment explanation
Indices: 194997--195071 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
194987 GTGAATGCAT
194997 ACATTTTCAGTTAGACATGCATTAGTAACTTGAGTTTGA
1 ACATTTTCAGTTAGACATGCATTAGTAACTTGAGTTTGA
*
195036 ACATTTTCAGTT-GAACATGCATTTGTAACTTGAGTT
1 ACATTTTCAGTTAG-ACATGCATTAGTAACTTGAGTT
195072 AAATTCGCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (39 bp):
ACATTTTCAGTTAGACATGCATTAGTAACTTGAGTTTGA
Found at i:195097 original size:20 final size:20
Alignment explanation
Indices: 195072--195127 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
195062 AACTTGAGTT
195072 AAATTCGCGTTGCGATAGTC
1 AAATTCGCGTTGCGATAGTC
* *
195092 AAATTCGC-TACGCGAAAGTC
1 AAATTCGCGT-TGCGATAGTC
*
195112 TAATTCGCGTTGCGAT
1 AAATTCGCGTTGCGAT
195128 TGTTGCGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (20 bp):
AAATTCGCGTTGCGATAGTC
Found at i:195154 original size:49 final size:49
Alignment explanation
Indices: 195080--195177 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
195070 TTAAATTCGC
* * * *
195080 GTTGCGATAGTCAAATTCGCTACGCGAAAGTCTAATTCGCGTTGCGATT
1 GTTGCGAAAGTCAAATTCGCAACGCGAAAATCAAATTCGCGTTGCGATT
*
195129 GTTGCGAAAGTCAAATTTGCAACGCGAAAATCAAATTCGCGTTGCGATT
1 GTTGCGAAAGTCAAATTCGCAACGCGAAAATCAAATTCGCGTTGCGATT
195178 TTCGCATTGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (49 bp):
GTTGCGAAAGTCAAATTCGCAACGCGAAAATCAAATTCGCGTTGCGATT
Found at i:195251 original size:20 final size:20
Alignment explanation
Indices: 195228--195274 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
195218 AAAATCAAAA
195228 CCGCAACGAGAATTTGACTT
1 CCGCAACGAGAATTTGACTT
** *
195248 CCGCATTGCGAATTTGACTT
1 CCGCAACGAGAATTTGACTT
*
195268 TCGCAAC
1 CCGCAAC
195275 AATCGCAACG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (20 bp):
CCGCAACGAGAATTTGACTT
Found at i:195306 original size:49 final size:50
Alignment explanation
Indices: 195229--195359 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 50
195219 AAATCAAAAC
* * * *
195229 CGCAACGAGAATTTGACTTCCGCATTGCGAATTTGACTTTCGCAA-CAAT
1 CGCAACGAGAATTTGACTTTCACGTTGCGAATTTGACTATCGCAACCAAT
* * * *
195278 CGCAACGTGAATTTGACTTTCACGTTGCGTATTTTACTATCGTAACGCAAT
1 CGCAACGAGAATTTGACTTTCACGTTGCGAATTTGACTATCGCAAC-CAAT
* * * *
195329 TGCAATGCGAATTTGACTTTCACGTTACGAA
1 CGCAACGAGAATTTGACTTTCACGTTGCGAA
195360 AGTGTACATT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
49 37 0.55
51 30 0.45
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (50 bp):
CGCAACGAGAATTTGACTTTCACGTTGCGAATTTGACTATCGCAACCAAT
Found at i:196833 original size:21 final size:19
Alignment explanation
Indices: 196807--196924 Score: 110
Period size: 21 Copynumber: 5.7 Consensus size: 19
196797 GTGAATCGGG
*
196807 CTCTTGAACGGTAGGAGGGAC
1 CTCTTGAACGAT-GGAGGG-C
*
196828 CTCTTGAACAATGAGAGAGGC
1 CTCTTGAACGATG-GAG-GGC
*
196849 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGAT-GGA-GGGC
196870 CTCTTGAACGATGAGAGGGAC
1 CTCTTGAACGATG-GAGGG-C
*
196891 CTCTTGAACAATAGGAGAGGC
1 CTCTTGAACGAT-GGAG-GGC
196912 CTCTTGAACGATG
1 CTCTTGAACGATG
196925 ACAGGTGAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
20 6 0.07
21 69 0.84
22 7 0.09
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.20
Consensus pattern (19 bp):
CTCTTGAACGATGGAGGGC
Found at i:196866 original size:42 final size:41
Alignment explanation
Indices: 196807--196925 Score: 159
Period size: 42 Copynumber: 2.8 Consensus size: 41
196797 GTGAATCGGG
*
196807 CTCTTGAACGGTAGGAGGGACCTCTTGAACAATGAGAGAGG-C
1 CTCTTGAACGGTAGGAGGG-CCTCTTGAACGATGAGAG-GGAC
*
196849 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGAC
1 CTCTTGAACGGTAGGA-GGGCCTCTTGAACGATGAGAGGGAC
**
196891 CTCTTGAACAATAGGAGAGGCCTCTTGAACGATGA
1 CTCTTGAACGGTAGGAG-GGCCTCTTGAACGATGA
196926 CAGGTGAATC
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
41 3 0.04
42 63 0.91
43 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.34, T:0.20
Consensus pattern (41 bp):
CTCTTGAACGGTAGGAGGGCCTCTTGAACGATGAGAGGGAC
Found at i:198913 original size:20 final size:20
Alignment explanation
Indices: 198890--198952 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
198880 AAACTTAAAT
198890 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
198910 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
198930 TCGCAACGTGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
198949 TCGC
1 TCGC
198953 GTTGCGAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 8 0.21
20 31 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:198990 original size:20 final size:20
Alignment explanation
Indices: 198953--198990 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
198943 CTAAAATCGC
* *
198953 GTTGCGAATTTCATTTTCGT
1 GTTGCGAATTTAAGTTTCGT
198973 GTTGCGAATTTAAGTTTC
1 GTTGCGAATTTAAGTTTC
198991 AAAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.47
Consensus pattern (20 bp):
GTTGCGAATTTAAGTTTCGT
Found at i:199357 original size:22 final size:22
Alignment explanation
Indices: 199328--199378 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
199318 ATAGAGGGGG
*
199328 GTCGCCGGATATGGGGACAGAT
1 GTCGCCGGAGATGGGGACAGAT
* *
199350 TTCGCCGGAGATGGGGACGGAT
1 GTCGCCGGAGATGGGGACAGAT
199372 GTCGCCG
1 GTCGCCG
199379 TAGAGAGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.22, G:0.43, T:0.18
Consensus pattern (22 bp):
GTCGCCGGAGATGGGGACAGAT
Found at i:199599 original size:19 final size:19
Alignment explanation
Indices: 199572--199613 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
199562 TGAGTTGCAA
* * *
199572 AATTGGAGTTCGCGTTGCG
1 AATTCGAGTTCACGTTACG
199591 AATTCGAGTTCACGTTACG
1 AATTCGAGTTCACGTTACG
199610 AATT
1 AATT
199614 TGTTGGTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (19 bp):
AATTCGAGTTCACGTTACG
Found at i:200584 original size:60 final size:60
Alignment explanation
Indices: 200472--200584 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 60
200462 GTCGGATGAT
* * *
200472 CATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACTATGTAATCACAGTAC
1 CATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACCATATAATCACAGTAC
* * * * * *
200532 CATTTTATAACTTTTAATAGTTGAGAGACTTAATAAATCAATACCCTATAATC
1 CATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACCATATAATC
200585 GGGGGGTCAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACCATATAATCACAGTAC
Found at i:202312 original size:18 final size:21
Alignment explanation
Indices: 202291--202331 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
202281 AGGTATTGAA
202291 TTTTGAATC-AAT-ATT-TGT
1 TTTTGAATCTAATGATTCTGT
202309 TTTTGAATCTAATGATTCTGT
1 TTTTGAATCTAATGATTCTGT
202330 TT
1 TT
202332 CTTGGATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 3 0.15
20 3 0.15
21 5 0.25
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.56
Consensus pattern (21 bp):
TTTTGAATCTAATGATTCTGT
Found at i:220876 original size:20 final size:22
Alignment explanation
Indices: 220849--220901 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
220839 CTAAACCTAG
**
220849 AGTATCGATACTC-CTTGAACA
1 AGTATCGATACTCTCAAGAACA
220870 A-TATCGATAC-CTCAAGAACA
1 AGTATCGATACTCTCAAGAACA
220890 AGTATCGATACT
1 AGTATCGATACT
220902 TCTACACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 16 0.59
21 10 0.37
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (22 bp):
AGTATCGATACTCTCAAGAACA
Found at i:230932 original size:23 final size:23
Alignment explanation
Indices: 230863--230943 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
230853 ACACCTAACA
*
230863 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
230885 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
230906 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
230929 GTGCATCGATGCACA
1 GTGCATCGATGCACA
230944 AGGTCATGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.32
22 10 0.21
23 21 0.45
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:230959 original size:43 final size:42
Alignment explanation
Indices: 230862--230961 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 42
230852 TACACCTAAC
* * *
230862 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGA
1 AGTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGA
* * *
230904 AGGTGCACCGATGCACGCCTTGAATGTGCATCGATGCACAAGGTC
1 A-GTGCATCGATGCA-GCCTTGAATGTGCATCGATACACAAGG-A
230949 A-TGCATCGATGCA
1 AGTGCATCGATGCA
230962 TCTGTCAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 1 0.02
43 23 0.48
44 23 0.48
45 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (42 bp):
AGTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGA
Found at i:239296 original size:4 final size:4
Alignment explanation
Indices: 239282--239361 Score: 97
Period size: 4 Copynumber: 20.0 Consensus size: 4
239272 ACATACATAC
* * * * *
239282 ATAT ATGT ATAT ATAT ATAT ACAT ATAC ATAT ATAT ATAC ATAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
239330 ATAT ATAT ATAT GTAT GTAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
239362 GTATGCAGTG
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 64 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (4 bp):
ATAT
Found at i:239298 original size:6 final size:6
Alignment explanation
Indices: 239282--239361 Score: 97
Period size: 6 Copynumber: 13.3 Consensus size: 6
239272 ACATACATAC
* * * * *
239282 ATATAT GTATAT ATATAT ATACAT ATACAT ATATAT ATACAT ATACAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* *
239330 ATATAT ATATAT GTATGT ATATAT ATATAT AT
1 ATATAT ATATAT ATATAT ATATAT ATATAT AT
239362 GTATGCAGTG
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (6 bp):
ATATAT
Found at i:240024 original size:24 final size:23
Alignment explanation
Indices: 239978--240026 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
239968 AAAATAAAAT
* *
239978 AAAAAAGTGTTATGAAAGCAGAG
1 AAAAAAGTGTTATAAAAACAGAG
*
240001 AAAAAACGTGTTATAAAAATAGAG
1 AAAAAA-GTGTTATAAAAACAGAG
240025 AA
1 AA
240027 TTTCATGTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.57, C:0.04, G:0.20, T:0.18
Consensus pattern (23 bp):
AAAAAAGTGTTATAAAAACAGAG
Found at i:240297 original size:34 final size:34
Alignment explanation
Indices: 240259--240329 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
240249 AAAAAAATTA
240259 CTCGAGCTTCAAAAAAACTTAATCTCGAAACATT
1 CTCGAGCTTCAAAAAAACTTAATCTCGAAACATT
240293 CTCGAGCTTCAAAAAAACTTAATCTCGAAACATT
1 CTCGAGCTTCAAAAAAACTTAATCTCGAAACATT
240327 CTC
1 CTC
240330 AAATTTAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.27
Consensus pattern (34 bp):
CTCGAGCTTCAAAAAAACTTAATCTCGAAACATT
Found at i:240799 original size:25 final size:26
Alignment explanation
Indices: 240771--240819 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
240761 AATATTTAAT
*
240771 TTGATT-TTAATGAAATTATTGATCA
1 TTGATTGTTAATAAAATTATTGATCA
240796 TTGATTGTTAATAAAATTATTGAT
1 TTGATTGTTAATAAAATTATTGAT
240820 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (26 bp):
TTGATTGTTAATAAAATTATTGATCA
Found at i:245230 original size:23 final size:23
Alignment explanation
Indices: 245195--245239 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
245185 AATGTTATCG
* * *
245195 ATCTATTCGATTCAGAATCCTCA
1 ATCTATCCCATTCAAAATCCTCA
245218 ATCTATCCCATTCAAAATCCTC
1 ATCTATCCCATTCAAAATCCTC
245240 TATCGTTAAC
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:0.31, C:0.31, G:0.04, T:0.33
Consensus pattern (23 bp):
ATCTATCCCATTCAAAATCCTCA
Found at i:250163 original size:19 final size:19
Alignment explanation
Indices: 250139--250186 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
250129 TAACAAAAAG
250139 AATGACTAGTTTAGAACAT
1 AATGACTAGTTTAGAACAT
250158 AATGACTAGTTTAGAACAT
1 AATGACTAGTTTAGAACAT
*
250177 AATGAATAGT
1 AATGACTAGT
250187 CGGGTGACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (19 bp):
AATGACTAGTTTAGAACAT
Found at i:252524 original size:83 final size:83
Alignment explanation
Indices: 252385--252552 Score: 327
Period size: 83 Copynumber: 2.0 Consensus size: 83
252375 ATTAGTTCTG
*
252385 GCGTTAGAGGCTTTCTTAAGCTTCCGTATTTACTGGAAGAAACCATTAGTTTAATGCGCCGGATT
1 GCGTTAGAGGCTTTCTTAAGCTTCCATATTTACTGGAAGAAACCATTAGTTTAATGCGCCGGATT
252450 CCGATCATAAAGCATACT
66 CCGATCATAAAGCATACT
252468 GCGTTAGAGGCTTTCTTAAGCTTCCATATTTACTGGAAGAAACCATTAGTTTAATGCGCCGGATT
1 GCGTTAGAGGCTTTCTTAAGCTTCCATATTTACTGGAAGAAACCATTAGTTTAATGCGCCGGATT
252533 CCGATCATAAAGCATACT
66 CCGATCATAAAGCATACT
252551 GC
1 GC
252553 TGATATCAGT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (83 bp):
GCGTTAGAGGCTTTCTTAAGCTTCCATATTTACTGGAAGAAACCATTAGTTTAATGCGCCGGATT
CCGATCATAAAGCATACT
Found at i:269178 original size:60 final size:57
Alignment explanation
Indices: 269022--269178 Score: 136
Period size: 60 Copynumber: 2.7 Consensus size: 57
269012 AAAGTCCAGG
* * * * *
269022 GATGGAATTAAAATATTTAAAAGTTTAAGGATTAATATAGAATGAGACATAGTTTGGA
1 GATGAAATTGAAATATTTAAAAGTTTAA-GATCAATTTAGAATAAGACATAGTTTGGA
* * * * * * * *
269080 GATGAATTTGAAACATTCAAAATTTTACGGATCGATTTAGAATAAATGTCATAGTTTGGG
1 GATGAAATTGAAATATTTAAAAGTTTA-AGATCAATTTAGAAT-AA-GACATAGTTTGGA
269140 GAAT-AAATTGAAATATTTAAAAGTTTAAGATCCAATTTA
1 G-ATGAAATTGAAATATTTAAAAGTTTAAGAT-CAATTTA
269179 AAGGACAAAT
Statistics
Matches: 75, Mismatches: 19, Indels: 8
0.74 0.19 0.08
Matches are distributed among these distances:
58 32 0.43
59 4 0.05
60 37 0.49
61 2 0.03
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (57 bp):
GATGAAATTGAAATATTTAAAAGTTTAAGATCAATTTAGAATAAGACATAGTTTGGA
Found at i:269514 original size:16 final size:17
Alignment explanation
Indices: 269493--269525 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
269483 TATTAAAAAA
269493 AATTG-ATGTCAATCTG
1 AATTGAATGTCAATCTG
*
269509 AATTGAATGTTAATCTG
1 AATTGAATGTCAATCTG
269526 TAGACTGGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (17 bp):
AATTGAATGTCAATCTG
Found at i:276215 original size:18 final size:18
Alignment explanation
Indices: 276192--276229 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
276182 TTTGTTAGGG
276192 TTTGAATTTTTAAACATT
1 TTTGAATTTTTAAACATT
276210 TTTGAATTTTTAAACATT
1 TTTGAATTTTTAAACATT
276228 TT
1 TT
276230 AGGGTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTGAATTTTTAAACATT
Found at i:279117 original size:60 final size:60
Alignment explanation
Indices: 279023--279138 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
279013 TTTTAGTATC
*
279023 AAATCATTATTATAATTTCATTACTAGTAATCATTAGTATCAAATAATTAAAATATTAATAAT
1 AAATCATTATTATAA-TTAATTACTAG-AATCATTAGTATCAAATAATT-AAATATTAATAAT
*
279086 AAATCATTATTAATAA-TAATTACTA-AATCATTAGTATCAAATTATTAAATATT
1 AAATCATTATT-ATAATTAATTACTAGAATCATTAGTATCAAATAATTAAATATT
279139 TAGAAATCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
59 7 0.14
60 20 0.40
62 8 0.16
63 11 0.22
64 4 0.08
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (60 bp):
AAATCATTATTATAATTAATTACTAGAATCATTAGTATCAAATAATTAAATATTAATAAT
Found at i:279254 original size:14 final size:14
Alignment explanation
Indices: 279237--279406 Score: 169
Period size: 14 Copynumber: 12.7 Consensus size: 14
279227 TAGTAATAAG
*
279237 TATTAAATCATTAG
1 TATTAAATCATTAT
*
279251 TATTAAATCATTAA
1 TATTAAATCATTAT
*
279265 TAATAAATCATTAT
1 TATTAAATCATTAT
*
279279 TATCAAATC---AT
1 TATTAAATCATTAT
*
279290 TACTAAATCATTAT
1 TATTAAATCATTAT
279304 TATTAAATCATTAT
1 TATTAAATCATTAT
*
279318 TA-T-AATGATTAT
1 TATTAAATCATTAT
279330 TATTAAATCATTAT
1 TATTAAATCATTAT
*
279344 TA-T-AATGATTAT
1 TATTAAATCATTAT
* *
279356 TATCAAATCATTAAA
1 TATTAAATCATT-AT
*
279371 TATTAAA--ATCAT
1 TATTAAATCATTAT
279383 TATTAAATCATTAT
1 TATTAAATCATTAT
*
279397 TATCAAATCA
1 TATTAAATCA
279407 GTACTAAATC
Statistics
Matches: 127, Mismatches: 19, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
11 9 0.07
12 28 0.22
13 5 0.04
14 78 0.61
15 7 0.06
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (14 bp):
TATTAAATCATTAT
Found at i:279381 original size:16 final size:16
Alignment explanation
Indices: 279360--279479 Score: 60
Period size: 16 Copynumber: 7.6 Consensus size: 16
279350 GATTATTATC
279360 AAATCATTAAATATTA
1 AAATCATTAAATATTA
279376 AAATCA-T---TATT-
1 AAATCATTAAATATTA
* *
279387 AAATCATT-ATTA-TC
1 AAATCATTAAATATTA
*
279401 AAATCAGTACTAAATCA-TC
1 AAATCA-T--TAAAT-ATTA
279420 AAATCATTAAATATTA
1 AAATCATTAAATATTA
*
279436 AAATCATTACTAA-ATCATC
1 AAATCATTA--AATAT--TA
*
279455 AAATAATTAAATATTA
1 AAATCATTAAATATTA
279471 AAATCATTA
1 AAATCATTA
279480 TTAAATCATT
Statistics
Matches: 83, Mismatches: 6, Indels: 30
0.70 0.05 0.25
Matches are distributed among these distances:
11 6 0.07
12 5 0.06
13 1 0.01
14 8 0.10
15 3 0.04
16 30 0.36
17 5 0.06
18 7 0.08
19 18 0.22
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.36
Consensus pattern (16 bp):
AAATCATTAAATATTA
Found at i:279389 original size:19 final size:19
Alignment explanation
Indices: 279365--279485 Score: 69
Period size: 19 Copynumber: 6.4 Consensus size: 19
279355 TTATCAAATC
279365 ATTAAATATTAAAATCATT
1 ATTAAATATTAAAATCATT
*
279384 ATTAAATCATTATTATCAAATCAGT
1 ATT-AA--A-TATTA--AAATCATT
* *
279409 ACTAAATCA-TCAAATC---
1 ATTAAAT-ATTAAAATCATT
279425 ATTAAATATTAAAATCATT
1 ATTAAATATTAAAATCATT
* *
279444 ACTAAATCA-TCAAAT-A--
1 ATTAAAT-ATTAAAATCATT
279460 ATTAAATATTAAAATCATT
1 ATTAAATATTAAAATCATT
279479 ATTAAAT
1 ATTAAAT
279486 CATTTTTATG
Statistics
Matches: 77, Mismatches: 9, Indels: 32
0.65 0.08 0.27
Matches are distributed among these distances:
15 2 0.03
16 23 0.30
17 1 0.01
18 1 0.01
19 26 0.34
20 3 0.04
21 2 0.03
22 3 0.04
23 5 0.06
24 2 0.03
25 9 0.12
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (19 bp):
ATTAAATATTAAAATCATT
Found at i:279447 original size:35 final size:35
Alignment explanation
Indices: 279401--279488 Score: 149
Period size: 35 Copynumber: 2.5 Consensus size: 35
279391 CATTATTATC
* *
279401 AAATCAGTACTAAATCATCAAATCATTAAATATTA
1 AAATCATTACTAAATCATCAAATAATTAAATATTA
279436 AAATCATTACTAAATCATCAAATAATTAAATATTA
1 AAATCATTACTAAATCATCAAATAATTAAATATTA
*
279471 AAATCATTATTAAATCAT
1 AAATCATTACTAAATCAT
279489 TTTTATGGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (35 bp):
AAATCATTACTAAATCATCAAATAATTAAATATTA
Found at i:279474 original size:8 final size:9
Alignment explanation
Indices: 279420--279489 Score: 51
Period size: 8 Copynumber: 7.9 Consensus size: 9
279410 CTAAATCATC
279420 AAATCATT-
1 AAATCATTA
279428 AAAT-ATTA
1 AAATCATTA
279436 AAATCATTA
1 AAATCATTA
*
279445 CTAAATCA-TC
1 --AAATCATTA
*
279455 AAATAATT-
1 AAATCATTA
279463 AAAT-ATTA
1 AAATCATTA
279471 AAATCATTA
1 AAATCATTA
279480 TTAAATCATT
1 --AAATCATT
279490 TTTATGGTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
7 6 0.12
8 21 0.41
9 9 0.18
10 1 0.02
11 14 0.27
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (9 bp):
AAATCATTA
Found at i:279768 original size:49 final size:49
Alignment explanation
Indices: 279696--279919 Score: 276
Period size: 49 Copynumber: 4.6 Consensus size: 49
279686 ATTACTAATA
* *
279696 ATTACTAAATTATTACTTTCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* *
279746 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCTTT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
279795 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* * * * **
279844 ATTGCTAATCATTACTA-AATAATTATTATAATTTTAA-ATATAAAATCATT
1 ATTACTAATCATTACTATCA-AATCATTA-AATATTAATA-ATAATTTCATT
* *
279894 ATTA--AATCATGATTATCAAATCATTA
1 ATTACTAATCATTACTATCAAATCATTA
279920 CTAAATCAAA
Statistics
Matches: 153, Mismatches: 17, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
48 17 0.11
49 111 0.73
50 25 0.16
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:281543 original size:19 final size:19
Alignment explanation
Indices: 281519--281562 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
281509 TCGCTTCATT
281519 GCTTGTAGTAAATGTGGTA
1 GCTTGTAGTAAATGTGGTA
281538 GCTTGTAGTAAATGTGGTA
1 GCTTGTAGTAAATGTGGTA
281557 GCTTGT
1 GCTTGT
281563 TGTACGATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.23, C:0.07, G:0.32, T:0.39
Consensus pattern (19 bp):
GCTTGTAGTAAATGTGGTA
Found at i:283056 original size:16 final size:17
Alignment explanation
Indices: 283022--283059 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
283012 TAATATAAAA
283022 TAAACACTAAATATTTT
1 TAAACACTAAATATTTT
283039 TAAACAC--AATATTTTT
1 TAAACACTAAATA-TTTT
283055 TAAAC
1 TAAAC
283060 GGGAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 9 0.45
17 7 0.35
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAACACTAAATATTTT
Found at i:283114 original size:83 final size:83
Alignment explanation
Indices: 282941--283102 Score: 290
Period size: 82 Copynumber: 2.0 Consensus size: 83
282931 TTTTTAAAAC
**
282941 AACACTAAATATTTTTAAACACTTTATTTTTTTAAACGAGAATAAATTAAACAAATTAATTTTAT
1 AACACTAAATATTTTTAAACACAATATTTTTTTAAACGAGAATAAATTAAACAAATTAATTTTAT
283006 ATAATCTAATATAAAATA
66 ATAATCTAATATAAAATA
*
283024 AACACTAAATATTTTTAAACACAATA-TTTTTTAAACGGGAATAAATTAAACAAATTAATTTTAT
1 AACACTAAATATTTTTAAACACAATATTTTTTTAAACGAGAATAAATTAAACAAATTAATTTTAT
283088 ATAATCTAATATAAA
66 ATAATCTAATATAAA
283103 CTAACTAACT
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
82 52 0.68
83 24 0.32
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (83 bp):
AACACTAAATATTTTTAAACACAATATTTTTTTAAACGAGAATAAATTAAACAAATTAATTTTAT
ATAATCTAATATAAAATA
Found at i:283625 original size:28 final size:28
Alignment explanation
Indices: 283560--283625 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
283550 TTTATATAAT
*
283560 CTAATATATAACTTAAACTATCAAACTA
1 CTAATATATAACTTAAACTAACAAACTA
*
283588 AT-ATAATATAACTTAAACTAACAAACTA
1 CTAAT-ATATAACTTAAACTAACAAACTA
*
283616 CTAATTTATA
1 CTAATATATA
283626 CTAACAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 28 0.88
29 2 0.06
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (28 bp):
CTAATATATAACTTAAACTAACAAACTA
Found at i:283780 original size:5 final size:5
Alignment explanation
Indices: 283770--283804 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
283760 TTCTTATTCT
283770 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC
283805 CTCGCCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTCC
Found at i:286966 original size:16 final size:16
Alignment explanation
Indices: 286947--286980 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
286937 CAATATACGA
286947 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
286963 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
286979 AT
1 AT
286981 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:287054 original size:16 final size:18
Alignment explanation
Indices: 287022--287055 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
287012 TATTAATGTA
287022 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
287040 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
287056 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:287729 original size:130 final size:130
Alignment explanation
Indices: 287525--287772 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
287515 AATTTTCTTC
* * *
287525 TAATTAGGTGGTGACAAGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGATGACAAGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
287590 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
287655 TAATTAGGTGATGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGATGACAAGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
287720 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
287773 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGATGACAAGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:288219 original size:35 final size:35
Alignment explanation
Indices: 288169--288244 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
288159 AATTGAATTT
* *
288169 AATTGAATTATTTTGG-AATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTGA-GGTTTAGAATGA
288204 AATTGAATTACTTTGGAAATTGAGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTGAGGTTTAGAATGA
288239 AATTGA
1 AATTGA
288245 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 33 0.87
36 5 0.13
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTGAGGTTTAGAATGA
Found at i:289406 original size:17 final size:18
Alignment explanation
Indices: 289367--289430 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 18
289357 CCGATCCGAT
289367 CCGTTGACGTTTT-GTTGA
1 CCGTTGAC-TTTTCGTTGA
289385 CCGTTGACTTTTCGTTGA
1 CCGTTGACTTTTCGTTGA
*
289403 -CGTTGACTTTTCATTGA
1 CCGTTGACTTTTCGTTGA
*
289420 CCATTGACTTT
1 CCGTTGACTTT
289431 GACCGTTGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.48
18 22 0.52
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (18 bp):
CCGTTGACTTTTCGTTGA
Found at i:290799 original size:31 final size:31
Alignment explanation
Indices: 290761--290865 Score: 156
Period size: 31 Copynumber: 3.4 Consensus size: 31
290751 AAAACATATT
* *
290761 TTTTGGTCACTTACGTTATTGTTTCATTAAG
1 TTTTGGTCACTTACGTTATTATTTTATTAAG
*
290792 TTTTGGTCACTTACGTTATTATTTTATTAGG
1 TTTTGGTCACTTACGTTATTATTTTATTAAG
* * *
290823 TTTTGGTCACTAACGTTATCATTTTATTAAT
1 TTTTGGTCACTTACGTTATTATTTTATTAAG
290854 TTTTGGTCACTT
1 TTTTGGTCACTT
290866 GGACGTTGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.53
Consensus pattern (31 bp):
TTTTGGTCACTTACGTTATTATTTTATTAAG
Found at i:295812 original size:279 final size:279
Alignment explanation
Indices: 295312--295872 Score: 1122
Period size: 279 Copynumber: 2.0 Consensus size: 279
295302 TATTTTACGA
295312 TATGTGATAATTTCGATTTAGTGAATAAACTTTATTTTAGCATTATTCATGTTCCTAATACTTCA
1 TATGTGATAATTTCGATTTAGTGAATAAACTTTATTTTAGCATTATTCATGTTCCTAATACTTCA
295377 GCGATGGCTTTAAAAAATGAGATATTTTATTCTTTCTTTATCCGAGATGTGATATAAAGATTATG
66 GCGATGGCTTTAAAAAATGAGATATTTTATTCTTTCTTTATCCGAGATGTGATATAAAGATTATG
295442 TTGGTACAATTCTAATCAAGTTGATAAATCCTTATAGACTTAAAGTACTCCTTAGGATGGCTCCT
131 TTGGTACAATTCTAATCAAGTTGATAAATCCTTATAGACTTAAAGTACTCCTTAGGATGGCTCCT
295507 ACAAACAATAAGTCTAGGGCAAGTCCTTATATATCTAAGATAACCCCTTAGGTTGGCTCCTATAT
196 ACAAACAATAAGTCTAGGGCAAGTCCTTATATATCTAAGATAACCCCTTAGGTTGGCTCCTATAT
295572 TTTGACTAGAGTAAGTCCT
261 TTTGACTAGAGTAAGTCCT
295591 TATGTGATAATTTCGATTTAGTGAATAAACTTTATTTTAGCATTATTCATGTTCCTAATACTTCA
1 TATGTGATAATTTCGATTTAGTGAATAAACTTTATTTTAGCATTATTCATGTTCCTAATACTTCA
295656 GCGATGGCTTTAAAAAATGAGATATTTTATTCTTTCTTTATCCGAGATGTGATATAAAGATTATG
66 GCGATGGCTTTAAAAAATGAGATATTTTATTCTTTCTTTATCCGAGATGTGATATAAAGATTATG
295721 TTGGTACAATTCTAATCAAGTTGATAAATCCTTATAGACTTAAAGTACTCCTTAGGATGGCTCCT
131 TTGGTACAATTCTAATCAAGTTGATAAATCCTTATAGACTTAAAGTACTCCTTAGGATGGCTCCT
295786 ACAAACAATAAGTCTAGGGCAAGTCCTTATATATCTAAGATAACCCCTTAGGTTGGCTCCTATAT
196 ACAAACAATAAGTCTAGGGCAAGTCCTTATATATCTAAGATAACCCCTTAGGTTGGCTCCTATAT
295851 TTTGACTAGAGTAAGTCCT
261 TTTGACTAGAGTAAGTCCT
295870 TAT
1 TAT
295873 AGACCTAAGA
Statistics
Matches: 282, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
279 282 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (279 bp):
TATGTGATAATTTCGATTTAGTGAATAAACTTTATTTTAGCATTATTCATGTTCCTAATACTTCA
GCGATGGCTTTAAAAAATGAGATATTTTATTCTTTCTTTATCCGAGATGTGATATAAAGATTATG
TTGGTACAATTCTAATCAAGTTGATAAATCCTTATAGACTTAAAGTACTCCTTAGGATGGCTCCT
ACAAACAATAAGTCTAGGGCAAGTCCTTATATATCTAAGATAACCCCTTAGGTTGGCTCCTATAT
TTTGACTAGAGTAAGTCCT
Found at i:297010 original size:22 final size:22
Alignment explanation
Indices: 296985--297038 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
296975 CCTCTTAATG
*
296985 GAACCATTCAGCACTGAATGTT
1 GAACCGTTCAGCACTGAATGTT
*
297007 GAACCGTTCAGCGCTGAATGTT
1 GAACCGTTCAGCACTGAATGTT
297029 GAACCGTTCA
1 GAACCGTTCA
297039 ACATTCAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (22 bp):
GAACCGTTCAGCACTGAATGTT
Found at i:297232 original size:15 final size:16
Alignment explanation
Indices: 297194--297234 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
297184 ACAGAGCCTC
*
297194 TGAATCATTCAACATT
1 TGAATCATTCAACACT
*
297210 TGAATCATTCAACGCT
1 TGAATCATTCAACACT
297226 T-AATCATTC
1 TGAATCATTC
297235 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:308184 original size:20 final size:19
Alignment explanation
Indices: 308161--308217 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
308151 ACAGTTTCCA
* *
308161 AATTCACAACTCGAATTAGG
1 AATTCGCAACTCGAATT-CG
* *
308181 AATTCGCAACACAGAAGTCG
1 AATTCGCAACTC-GAATTCG
308201 AATTCGCAACTCGAATT
1 AATTCGCAACTCGAATT
308218 TGACAATTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.13
20 22 0.73
21 4 0.13
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (19 bp):
AATTCGCAACTCGAATTCG
Found at i:308308 original size:60 final size:60
Alignment explanation
Indices: 308225--308372 Score: 154
Period size: 60 Copynumber: 2.5 Consensus size: 60
308215 ATTTGACAAT
* *** * *
308225 TTCGCAAAACGAATTTTTTTTTCGCAA-ACCGAATTTCGTTTTCGTAACAAGATTTTCTAA
1 TTCGCAACACGAATTTAAATTTCGCAACA-CGAATTTCGTTTTCGCAACAAGATTTTCGAA
* * * * **
308285 TTCGCAACGCGAGTTTCAATTTCGCAACACGGATTTCGTTTTCGCAACTCGATTTTCGAA
1 TTCGCAACACGAATTTAAATTTCGCAACACGAATTTCGTTTTCGCAACAAGATTTTCGAA
* *
308345 TTTGCAACACGAATTTAAATTTCTCAAC
1 TTCGCAACACGAATTTAAATTTCGCAAC
308373 CCAGCCTTTA
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
60 70 0.99
61 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (60 bp):
TTCGCAACACGAATTTAAATTTCGCAACACGAATTTCGTTTTCGCAACAAGATTTTCGAA
Found at i:308329 original size:40 final size:40
Alignment explanation
Indices: 308285--308360 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
308275 GATTTTCTAA
*
308285 TTCGCAACGCGAGTTTC-AATTTCGCAACACGGATTTCGTT
1 TTCGCAACGCGAGTTTCGAATTT-GCAACACGAATTTCGTT
* *
308325 TTCGCAACTCGATTTTCGAATTTGCAACACGAATTT
1 TTCGCAACGCGAGTTTCGAATTTGCAACACGAATTT
308361 AAATTTCTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 27 0.84
41 5 0.16
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (40 bp):
TTCGCAACGCGAGTTTCGAATTTGCAACACGAATTTCGTT
Found at i:308341 original size:20 final size:20
Alignment explanation
Indices: 308224--308356 Score: 78
Period size: 20 Copynumber: 6.7 Consensus size: 20
308214 AATTTGACAA
* *
308224 TTTCGCAAAACGAATTTT-TT
1 TTTCGCAACACG-ATTTTCGT
*
308244 TTTCGCAA-ACCGAATTTCGT
1 TTTCGCAACA-CGATTTTCGT
* *
308264 TTTCGTAACAAGATTTTC-T
1 TTTCGCAACACGATTTTCGT
* * * **
308283 AATTCGCAACGCGAGTTTCAA
1 -TTTCGCAACACGATTTTCGT
308304 TTTCGCAACACGGA-TTTCGT
1 TTTCGCAACAC-GATTTTCGT
* *
308324 TTTCGCAACTCGATTTTCGAA
1 TTTCGCAACACGATTTTCG-T
308345 TTT-GCAACACGA
1 TTTCGCAACACGA
308357 ATTTAAATTT
Statistics
Matches: 87, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
19 8 0.09
20 73 0.84
21 6 0.07
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (20 bp):
TTTCGCAACACGATTTTCGT
Found at i:312686 original size:9 final size:9
Alignment explanation
Indices: 312672--312707 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
312662 CCTCTTTAAT
312672 TTTTTTTTC
1 TTTTTTTTC
312681 TTTTTTTTC
1 TTTTTTTTC
312690 TTTTTTTTTC
1 -TTTTTTTTC
312700 TTTTTTTT
1 TTTTTTTT
312708 ACTAACCCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:312686 original size:10 final size:10
Alignment explanation
Indices: 312671--312707 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
312661 CCCTCTTTAA
312671 TTTTTTTTTC
1 TTTTTTTTTC
312681 -TTTTTTTTC
1 TTTTTTTTTC
312690 TTTTTTTTTC
1 TTTTTTTTTC
312700 TTTTTTTT
1 TTTTTTTT
312708 ACTAACCCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:312695 original size:19 final size:19
Alignment explanation
Indices: 312671--312707 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
312661 CCCTCTTTAA
312671 TTTTTTTTTCTTTTTTTTC
1 TTTTTTTTTCTTTTTTTTC
312690 TTTTTTTTTCTTTTTTTT
1 TTTTTTTTTCTTTTTTTT
312708 ACTAACCCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (19 bp):
TTTTTTTTTCTTTTTTTTC
Found at i:313033 original size:17 final size:17
Alignment explanation
Indices: 313008--313050 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
312998 GTGAAGTATG
* *
313008 AATGGTGTTGTTGTGGC
1 AATGTTGTTGTCGTGGC
*
313025 AATGTTGTTGTCGTGGT
1 AATGTTGTTGTCGTGGC
313042 AAGTGTTGT
1 AA-TGTTGT
313051 AAGGTTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.14, C:0.05, G:0.37, T:0.44
Consensus pattern (17 bp):
AATGTTGTTGTCGTGGC
Found at i:318687 original size:14 final size:14
Alignment explanation
Indices: 318668--318710 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 14
318658 GAGGGAGGGC
318668 GAGAGAGAGTGGGAGA
1 GAGAGAGAGT-GG-GA
318684 GAGAGAGAGTGGGA
1 GAGAGAGAGTGGGA
318698 GAGAGAGAGTGGG
1 GAGAGAGAGTGGG
318711 CAAGAGTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 15 0.56
15 2 0.07
16 10 0.37
ACGTcount: A:0.35, C:0.00, G:0.58, T:0.07
Consensus pattern (14 bp):
GAGAGAGAGTGGGA
Found at i:318689 original size:16 final size:16
Alignment explanation
Indices: 318668--318706 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
318658 GAGGGAGGGC
318668 GAGAGAGAGTGGGAGA
1 GAGAGAGAGTGGGAGA
318684 GAGAGAGAGTGGGAGA
1 GAGAGAGAGTGGGAGA
318700 GAGAGAG
1 GAGAGAG
318707 TGGGCAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.56, T:0.05
Consensus pattern (16 bp):
GAGAGAGAGTGGGAGA
Found at i:318716 original size:14 final size:15
Alignment explanation
Indices: 318664--318716 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 15
318654 GAGGGAGGGA
318664 GGGC-GAGAGAGAGT
1 GGGCAGAGAGAGAGT
*
318678 GGGAGAGAGAGAGAGT
1 GGG-CAGAGAGAGAGT
318694 GGG-AGAGAGAGAGT
1 GGGCAGAGAGAGAGT
318708 GGGCA-AGAG
1 GGGCAGAGAG
318717 TGGGAGAGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
14 21 0.60
15 1 0.03
16 13 0.37
ACGTcount: A:0.34, C:0.04, G:0.57, T:0.06
Consensus pattern (15 bp):
GGGCAGAGAGAGAGT
Found at i:318716 original size:16 final size:15
Alignment explanation
Indices: 318668--318716 Score: 73
Period size: 16 Copynumber: 3.2 Consensus size: 15
318658 GAGGGAGGGC
318668 GAGAGAGAGTGGGAGA
1 GAGAGAGAGTGGGA-A
318684 GAGAGAGAGTGGG-A
1 GAGAGAGAGTGGGAA
318698 GAGAGAGAGTGGGCAA
1 GAGAGAGAGTGGG-AA
318714 GAG
1 GAG
318717 TGGGAGAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 14 0.45
16 17 0.55
ACGTcount: A:0.37, C:0.02, G:0.55, T:0.06
Consensus pattern (15 bp):
GAGAGAGAGTGGGAA
Found at i:319727 original size:21 final size:21
Alignment explanation
Indices: 319676--319727 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
319666 TGGCCTTACA
*
319676 GTATCGATAATGATCTCTAGT
1 GTATCGATACTGATCTCTAGT
319697 GTATCGATACTGATCTCTAGT
1 GTATCGATACTGATCTCTAGT
319718 GTATCGATAC
1 GTATCGATAC
319728 CCTCACTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (21 bp):
GTATCGATACTGATCTCTAGT
Found at i:320799 original size:21 final size:21
Alignment explanation
Indices: 320773--320815 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
320763 GGATTGCAAA
320773 TATTACCCCTAG-TATCGATAC
1 TATTA-CCCTAGATATCGATAC
*
320794 TATTACCCTCGATATCGATAC
1 TATTACCCTAGATATCGATAC
320815 T
1 T
320816 CCCCCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (21 bp):
TATTACCCTAGATATCGATAC
Found at i:320899 original size:20 final size:20
Alignment explanation
Indices: 320866--320904 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
320856 AAATGATCCA
320866 GTTCAACCAATATCGATAAT
1 GTTCAACCAATATCGATAAT
* *
320886 GTTCATCCAGTATCGATAA
1 GTTCAACCAATATCGATAA
320905 ACTAACAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (20 bp):
GTTCAACCAATATCGATAAT
Found at i:323965 original size:8 final size:8
Alignment explanation
Indices: 323952--323977 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
323942 GAAGAACGAG
323952 AGAGAGAA
1 AGAGAGAA
323960 AGAGAGAA
1 AGAGAGAA
323968 AGAGAGAA
1 AGAGAGAA
323976 AG
1 AG
323978 TGTGAGATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (8 bp):
AGAGAGAA
Found at i:324034 original size:32 final size:31
Alignment explanation
Indices: 323998--324060 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
323988 TGAGCGAGAG
* *
323998 AGAGTT-GACAAGAGTGAGGGAGAGAGTGAAAA
1 AGAGTTAG-CAAGAGTGAGAGAAAGAGT-AAAA
324030 AGAGTTAGCAAGAGTGAGAGAAAGAGTAAAA
1 AGAGTTAGCAAGAGTGAGAGAAAGAGTAAAA
324061 GATAGAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 4 0.14
32 23 0.82
33 1 0.04
ACGTcount: A:0.48, C:0.03, G:0.37, T:0.13
Consensus pattern (31 bp):
AGAGTTAGCAAGAGTGAGAGAAAGAGTAAAA
Found at i:325947 original size:23 final size:23
Alignment explanation
Indices: 325921--325964 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
325911 ATCGGTCACA
325921 ACCCGACCCGACCCGTTGACCCG
1 ACCCGACCCGACCCGTTGACCCG
325944 ACCCGACCCGACCCGTTGACC
1 ACCCGACCCGACCCGTTGACC
325965 GTTGATAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.52, G:0.20, T:0.09
Consensus pattern (23 bp):
ACCCGACCCGACCCGTTGACCCG
Found at i:331517 original size:27 final size:27
Alignment explanation
Indices: 331478--331545 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
331468 GTGTAGGAAT
331478 TATAGA-A-ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
331503 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
331530 TATAGAGATATGATTT
1 TATAGAGATATGATTT
331546 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 6 0.15
26 1 0.02
27 34 0.83
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:336233 original size:20 final size:20
Alignment explanation
Indices: 336208--336253 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
336198 ATCTGTATTA
336208 CTCGATTTGGATATCGAGTG
1 CTCGATTTGGATATCGAGTG
336228 CTCGATTTGGATATCGAGTG
1 CTCGATTTGGATATCGAGTG
336248 CTCGAT
1 CTCGAT
336254 ACGAGTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (20 bp):
CTCGATTTGGATATCGAGTG
Found at i:340299 original size:2 final size:2
Alignment explanation
Indices: 340287--340322 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
340277 GTAAAAGGGC
*
340287 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
340323 GTCATCCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:347289 original size:11 final size:11
Alignment explanation
Indices: 347273--347297 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
347263 ACAATAAGGT
347273 TTTTGAAATGA
1 TTTTGAAATGA
347284 TTTTGAAATGA
1 TTTTGAAATGA
347295 TTT
1 TTT
347298 ATTGGAATGT
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (11 bp):
TTTTGAAATGA
Found at i:349625 original size:3 final size:3
Alignment explanation
Indices: 349617--349677 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
349607 TGTTATTTAT
*
349617 TTA TTA TTA GT- TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
349663 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
349678 ATAAATAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 3 0.06
3 51 0.94
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:349651 original size:26 final size:26
Alignment explanation
Indices: 349617--349677 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 26
349607 TGTTATTTAT
349617 TTATTATTAGTT-TATTATTATTATTA
1 TTATTATTA-TTATATTATTATTATTA
349643 TTATTATTATTATATTATTATTATTA
1 TTATTATTATTATATTATTATTATTA
349669 TTATTATTA
1 TTATTATTA
349678 ATAAATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 2 0.06
26 32 0.94
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (26 bp):
TTATTATTATTATATTATTATTATTA
Found at i:354136 original size:14 final size:14
Alignment explanation
Indices: 354118--354155 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
354108 ACATCTTTGC
354118 ATTTGCATTTGCAT
1 ATTTGCATTTGCAT
*
354132 CTTTGCATTTGCAT
1 ATTTGCATTTGCAT
*
354146 ATTTGTATTT
1 ATTTGCATTT
354156 ACATTTTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.55
Consensus pattern (14 bp):
ATTTGCATTTGCAT
Found at i:356409 original size:89 final size:90
Alignment explanation
Indices: 356298--356475 Score: 277
Period size: 89 Copynumber: 2.0 Consensus size: 90
356288 GTTGGAGGCG
* * *
356298 TATATTCATTATATATGCAATAAAGCTTGAGTTATCCCCCTAAAACAATTGGTTAATCGCCTTGG
1 TATATTCATTATATATACAATAAAGCTTGAGTTATCCCCCTAAAACAATTGGTTAATAGCCCTGG
*
356363 CTTTATGGATATTATTCAGCTAGCC
66 CTTTATGGATAATATTCAGCTAGCC
* * * *
356388 TATATT-ATTATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAATAGCCCTGG
1 TATATTCATTATATATACAATAAAGCTTGAGTTATCCCCCTAAAACAATTGGTTAATAGCCCTGG
356452 CTTTATGGATAATATTCAGCTAGC
66 CTTTATGGATAATATTCAGCTAGC
356476 TTGTTATACT
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 74 0.93
90 6 0.08
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (90 bp):
TATATTCATTATATATACAATAAAGCTTGAGTTATCCCCCTAAAACAATTGGTTAATAGCCCTGG
CTTTATGGATAATATTCAGCTAGCC
Found at i:356584 original size:84 final size:84
Alignment explanation
Indices: 356329--356562 Score: 206
Period size: 89 Copynumber: 2.7 Consensus size: 84
356319 AAAGCTTGAG
* * * * ** * * *
356329 TTATCCCCCTAAAACAATTGGTTAATCGCCTTGGCTTTATGGATATTATTCAGCTAGCCT-ATAT
1 TTATCCCTCTAGAGCAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAACTAGCCTGTTA-
*
356393 TATTAT-ATATACAATAAAGCTTGA
65 TACTATAATATACAATAAA-----A
* * * *
356417 GTTGTCCCTCTAGAGCAATTGGTTAATAGCCCTGGCTTTATGGATAATATTCAGCTAGCTTGTTA
1 -TTATCCCTCTAGAGCAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAACTAGCCTGTTA
* *
356482 TACTATTATATGCAATAAAA
65 TACTATAATATACAATAAAA
*
356502 TTATCCCTCTAGAGCAATTGGTTAATTA-CCCCGGCTTTATGGATAAGT-TTCAATTAGCCTG
1 TTATCCCTCTAGAGCAATTGGTTAA-TAGCCCCGGCTTTATGGATAA-TATTCAACTAGCCTG
356563 ATTAAGGCAA
Statistics
Matches: 125, Mismatches: 16, Indels: 13
0.81 0.10 0.08
Matches are distributed among these distances:
84 51 0.41
85 4 0.03
89 57 0.46
90 13 0.10
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (84 bp):
TTATCCCTCTAGAGCAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAACTAGCCTGTTAT
ACTATAATATACAATAAAA
Found at i:357465 original size:36 final size:36
Alignment explanation
Indices: 357382--357468 Score: 131
Period size: 36 Copynumber: 2.4 Consensus size: 36
357372 ATGATCCATG
* * *
357382 TGGGGCATTTTGAAAGCTCACATTAGTATGAAAGTT
1 TGGGGCATTTTGAAGGCTCACATCAGTATGAAAATT
357418 TGGGGCATTTTGAAGGCTCACATCAGTATGAAAATT
1 TGGGGCATTTTGAAGGCTCACATCAGTATGAAAATT
357454 T-GGGCATTTTTGAAG
1 TGGGGCA-TTTTGAAG
357469 ACTCTTATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 5 0.11
36 42 0.89
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.33
Consensus pattern (36 bp):
TGGGGCATTTTGAAGGCTCACATCAGTATGAAAATT
Found at i:359024 original size:123 final size:123
Alignment explanation
Indices: 358658--359304 Score: 864
Period size: 123 Copynumber: 5.3 Consensus size: 123
358648 TCGAGGGATC
358658 ACCATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT-GTC
1 ACCATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTC
* * * * *
358722 TGAAGATCTTATTCAACCTTTTGCTTGAATCTATCACAGAAGAAGATAGAGCAGTAAA
66 TGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGCAAA
** * **
358780 ATAATATCCAGGGAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTT--T--T-
1 ACCATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTC
* * *
358840 T-AGAGAACTTATTCAACCTTTTGCTTGACTCTATCGCATAAGGAGATAGAGAAACAAA
66 TGA-AGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGCAAA
* * *
358898 ACCATCTCCAGACATAGTTCGTAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAGTC
1 ACCATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTC
* * *
358963 TGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAAGAGATAGAGCAGTAGA
66 TGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGCAAA
* * * * * *
359021 ACCATTTCTAGACAGAGTTCATCATAAGAAGAACTCATCCGAATAAGAAGAAGAAGTTCATAGTC
1 ACCATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTC
*
359086 TGAAGAACTTATTCAACCTTTTACTTGACTCTATCGCAGAAGGAGATAGAGCAAG-AAA
66 TGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGC-AGCAAA
* * *
359144 ACCATTTCCAGATAGAGTTTGTAATAAGAAGAACTCATCTGAAGAGGAAGAATAAGTTCATAGTC
1 ACCATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTC
* * * * * *
359209 TGAAAAACTTATTCAACCTTTTGCTCGACGCTATTGCAGAAGGAGATAGAGCAACATCA
66 TGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGCA-AA
*
359268 A-CGTTTCCAG-CAGAAGTTCGTAATAAGAAGAACTCAT
1 ACCATTTCCAGACAG-AGTTCGTAATAAGAAGAACTCAT
359305 TGTCTTTCGT
Statistics
Matches: 457, Mismatches: 57, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
117 1 0.00
118 99 0.22
119 1 0.00
120 2 0.00
122 57 0.12
123 292 0.64
124 5 0.01
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (123 bp):
ACCATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTC
TGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGCAAA
Found at i:359451 original size:3 final size:3
Alignment explanation
Indices: 359443--359505 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
359433 TCTTATTTAT
*
359443 TTA TTA TTA TTCA TTT TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
359488 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
359506 AATAATAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:360895 original size:5 final size:5
Alignment explanation
Indices: 360885--360914 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
360875 AAATTATTAT
360885 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
360915 GTCATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:362684 original size:44 final size:44
Alignment explanation
Indices: 362574--362689 Score: 133
Period size: 44 Copynumber: 2.6 Consensus size: 44
362564 TTGATGTTGT
** * * * *
362574 TCCAACTTATTATGTGATGGAAACAAGCGAAGTCATGATGTTGA
1 TCCAACTCCTTATGTGATGGAATCGAGCGAAGTCATAATGATGA
** * *
362618 TCCAACTCCTTATGCAATGGAATCGAGTGAAGTGATAATGATGA
1 TCCAACTCCTTATGTGATGGAATCGAGCGAAGTCATAATGATGA
*
362662 TCTAACTCCTTATGTGATGGAATCGAGC
1 TCCAACTCCTTATGTGATGGAATCGAGC
362690 AAAATGTTGA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29
Consensus pattern (44 bp):
TCCAACTCCTTATGTGATGGAATCGAGCGAAGTCATAATGATGA
Found at i:362707 original size:44 final size:44
Alignment explanation
Indices: 362574--362737 Score: 125
Period size: 44 Copynumber: 3.8 Consensus size: 44
362564 TTGATGTTGT
** * * * * * * *
362574 TCCAACTTATTATGTGATGGAAACAAGCGAAGTCATGATGTTGA
1 TCCAACTCCTTATGTGATGGAATCGAGCAAAATGATAATGATGA
** ** *
362618 TCCAACTCCTTATGCAATGGAATCGAGTGAAGTGATAATGATGA
1 TCCAACTCCTTATGTGATGGAATCGAGCAAAATGATAATGATGA
* * *
362662 TCTAACTCCTTATGTGATGGAATCGAGCAAAATGTTGAT-ACTGA
1 TCCAACTCCTTATGTGATGGAATCGAGCAAAATGATAATGA-TGA
* * *
362706 TCCAAC-CCTTATATGATGGAATTGAACAAAAT
1 TCCAACTCCTTATGTGATGGAATCGAGCAAAAT
362738 ATCGAACATG
Statistics
Matches: 97, Mismatches: 22, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
43 24 0.25
44 73 0.75
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (44 bp):
TCCAACTCCTTATGTGATGGAATCGAGCAAAATGATAATGATGA
Found at i:363006 original size:21 final size:22
Alignment explanation
Indices: 362982--363023 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
362972 AACAATTCTT
*
362982 CTCATTAGA-AAATTCTTCTCC
1 CTCATCAGATAAATTCTTCTCC
*
363003 CTCATCAGATAAGTTCTTCTC
1 CTCATCAGATAAATTCTTCTC
363024 ATTATGAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.26, C:0.29, G:0.07, T:0.38
Consensus pattern (22 bp):
CTCATCAGATAAATTCTTCTCC
Found at i:363047 original size:114 final size:113
Alignment explanation
Indices: 362741--363162 Score: 426
Period size: 115 Copynumber: 3.7 Consensus size: 113
362731 ACAAAATATC
* * * * * * *
362741 GAACATGTTCTTCTTATTAG-GAGTTCTTTCTCCCTTATCGGACAAGTTTTTCTCATTATGAACC
1 GAACAAGTTCTTCTCATTAGAAACTT-TTTCTCCCTCATCGGATAAGTTCTTCTCATTATGAACC
* * * *
362805 CTTCCACTGGAAATGTTTGATCCACCTTCTTTTGTGATGGATTCCAAGGTC
65 CTTCCACTAGAAATG-TTGATCCA-CTTCTTTTGTGATTGATGCCAAGGTT
* * * * *
362856 GAACAAGTTCTTATCATTAGTAACTTTTTCTCCCTCATCGAATTAGTTCTTCTCATTATAAACCC
1 GAACAAGTTCTTCTCATTAGAAACTTTTTCTCCCTCATCGGATAAGTTCTTCTCATTATGAACCC
*
362921 TTTCAC-AGGAAATGTTCGATCCACTTTCTTTTGTGATTGATGCCAAGGTT
66 TTCCACTA-GAAATGTT-GATCCAC-TTCTTTTGTGATTGATGCCAAGGTT
* * * *
362971 AAACAA-TTCTTCTCATTAGAAAATTCTTCTCCCTCATCAGATAAGTTCTTCTCATTATGAACCC
1 GAACAAGTTCTTCTCATTAGAAACTTTTTCTCCCTCATCGGATAAGTTCTTCTCATTATGAACCC
* ** *
363035 TTCCACTAGAAATGTTGATCCAC--CTCTTGTGA-TGTATGAAAAATGTT
66 TTCCACTAGAAATGTTGATCCACTTCTTTTGTGATTG-ATG-CCAAGGTT
* * * * *
363082 GAACAAGTTCTTCTCATTAGGAACTTTTTCTCTCTCATTGGATGAGTTCTTCTTATTATGAA-CC
1 GAACAAGTTCTTCTCATTAGAAACTTTTTCTCCCTCATCGGATAAGTTCTTCTCATTATGAACCC
* *
363146 TCTCCATTAAAAATGTT
66 T-TCCACTAGAAATGTT
363163 TGGTCTATAT
Statistics
Matches: 257, Mismatches: 41, Indels: 21
0.81 0.13 0.07
Matches are distributed among these distances:
109 2 0.01
110 11 0.04
111 13 0.05
112 60 0.23
113 7 0.03
114 66 0.26
115 95 0.37
116 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (113 bp):
GAACAAGTTCTTCTCATTAGAAACTTTTTCTCCCTCATCGGATAAGTTCTTCTCATTATGAACCC
TTCCACTAGAAATGTTGATCCACTTCTTTTGTGATTGATGCCAAGGTT
Found at i:365858 original size:18 final size:20
Alignment explanation
Indices: 365825--365863 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
365815 ATAATCGTCT
365825 AAAAACAAATGATAAA-AAA
1 AAAAACAAATGATAAACAAA
365844 AAAAACAAATG-TAAACAAA
1 AAAAACAAATGATAAACAAA
365863 A
1 A
365864 CATGAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.77, C:0.08, G:0.05, T:0.10
Consensus pattern (20 bp):
AAAAACAAATGATAAACAAA
Found at i:367852 original size:20 final size:20
Alignment explanation
Indices: 367827--367923 Score: 86
Period size: 20 Copynumber: 4.8 Consensus size: 20
367817 ATTCGCGTTG
*
367827 CATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTC
*
367847 CATTTCGCATTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* * * *
367867 CAGTTCGCGTTGCAATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
367888 AAAATCGTGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
*
367908 TATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
367924 AGTCTACAGT
Statistics
Matches: 58, Mismatches: 18, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:368703 original size:22 final size:22
Alignment explanation
Indices: 368677--368719 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
368667 AATCGTAACG
368677 ACAACTGTAGACTATCACAACA
1 ACAACTGTAGACTATCACAACA
*
368699 ACAACTGTAGACTATCGCAAC
1 ACAACTGTAGACTATCACAAC
368720 GCGAAATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.19
Consensus pattern (22 bp):
ACAACTGTAGACTATCACAACA
Found at i:368772 original size:21 final size:21
Alignment explanation
Indices: 368709--368773 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
368699 ACAACTGTAG
*
368709 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
368730 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
368750 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
368771 ACT
1 ACT
368774 CGAATTTGCA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:373393 original size:17 final size:17
Alignment explanation
Indices: 373373--373407 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
373363 ACAAGTGACT
* *
373373 AAATTGAAACAGATGCA
1 AAATTAAAACACATGCA
373390 AAATTAAAACACATGCA
1 AAATTAAAACACATGCA
373407 A
1 A
373408 TTGAAGAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.14, G:0.11, T:0.17
Consensus pattern (17 bp):
AAATTAAAACACATGCA
Found at i:374639 original size:21 final size:22
Alignment explanation
Indices: 374613--374661 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
374603 AATTTACTAG
*
374613 TTTTTTAATTTAATC-TTTTAA
1 TTTTTTAATTTAATCAATTTAA
* *
374634 TTTTTTATTTTATTCAATTTAA
1 TTTTTTAATTTAATCAATTTAA
374656 TTTTTT
1 TTTTTT
374662 GACTGCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTAATTTAATCAATTTAA
Found at i:374815 original size:2 final size:2
Alignment explanation
Indices: 374808--374868 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
374798 TATAATATGA
374808 AT AT AT 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 AT AT AT
374850 AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
374869 CTTATATGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:375332 original size:26 final size:27
Alignment explanation
Indices: 375303--375363 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
375293 ATCTTTAATA
375303 ACAATATAAAT-TAT-TGATATATATAT
1 ACAATATAAATATATAT-ATATATATAT
375329 ACAA-ATTAAAATATATATATATATATAT
1 ACAATA-T-AAATATATATATATATATAT
375357 A-AATATA
1 ACAATATA
375364 TTTTATGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
25 1 0.03
26 6 0.20
27 7 0.23
28 15 0.50
29 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (27 bp):
ACAATATAAATATATATATATATATAT
Found at i:382526 original size:20 final size:20
Alignment explanation
Indices: 382503--382544 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
382493 CATTCTAACT
382503 TCAAATT-CAGCATTAAAACA
1 TCAAATTCCAGCATT-AAACA
*
382523 TCAATTTCCAGCATTAAACA
1 TCAAATTCCAGCATTAAACA
382543 TC
1 TC
382545 CCTAATTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.29
Consensus pattern (20 bp):
TCAAATTCCAGCATTAAACA
Found at i:383797 original size:2 final size:2
Alignment explanation
Indices: 383790--383816 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
383780 GGGTATTACA
383790 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
383817 ATTTTCACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:386256 original size:3 final size:3
Alignment explanation
Indices: 386248--386274 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
386238 CTACCCATAT
386248 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
386275 GAGAATAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:386488 original size:15 final size:15
Alignment explanation
Indices: 386464--386497 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
386454 AAACAAGTTT
*
386464 GTAGCGGTGGTTTTA
1 GTAGCAGTGGTTTTA
386479 GTAGCAGTGGTTTTA
1 GTAGCAGTGGTTTTA
386494 GTAG
1 GTAG
386498 GTTTTTAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.38, T:0.38
Consensus pattern (15 bp):
GTAGCAGTGGTTTTA
Found at i:389618 original size:43 final size:43
Alignment explanation
Indices: 389570--389748 Score: 209
Period size: 43 Copynumber: 4.2 Consensus size: 43
389560 ATTACCTACA
* * *
389570 TATTGTGGCGTTTGTAAGAAAAACATCGCTAAATATATGAACC
1 TATTGTGGCATTTGTAAGAAAAACACCGCTAAATGTATGAACC
* * * * * *
389613 TATTGTGACATTTATAATAAAAACAACGCTAAATGTCTAAACC
1 TATTGTGGCATTTGTAAGAAAAACACCGCTAAATGTATGAACC
* *
389656 TATTGCGGCATTTGTAAGAAAAACGCCGCTAAATGTATGAACC
1 TATTGTGGCATTTGTAAGAAAAACACCGCTAAATGTATGAACC
* * * *
389699 TATTGCGGCATTTGT-A-AAAAGCGCCGCTAAATGTCTGAACC
1 TATTGTGGCATTTGTAAGAAAAACACCGCTAAATGTATGAACC
389740 TATTGTGGC
1 TATTGTGGC
389749 GCTTTTTATT
Statistics
Matches: 117, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
41 31 0.26
42 1 0.01
43 85 0.73
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (43 bp):
TATTGTGGCATTTGTAAGAAAAACACCGCTAAATGTATGAACC
Found at i:396383 original size:17 final size:18
Alignment explanation
Indices: 396358--396397 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
396348 AATTTATTTA
396358 ATAATATATTTTATACAT
1 ATAATATATTTTATACAT
*
396376 ATAA-ATATTTTATAGAT
1 ATAATATATTTTATACAT
396393 ATAAT
1 ATAAT
396398 TCTTTGAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
ATAATATATTTTATACAT
Found at i:397869 original size:339 final size:337
Alignment explanation
Indices: 397183--398194 Score: 1603
Period size: 339 Copynumber: 3.0 Consensus size: 337
397173 CAACTCATAA
* **
397183 ATTTTGATTTTTGCATGAAATTATACAATACATATAATCTAGTATAAAAAAACTTTGAGGGTAAA
1 ATTTTGATTTTTGCATGAAATTACACAATACATATAATCTAGTATAGGAAAACTTTGAGGGTAAA
397248 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTCTTTT---ATAA--A--A
66 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTCTTTTACAATAATGATGA
* * *
397306 TGATGATGATGATAAATATTTTATTA-TTAACAAATTATAAATTTCATATATTTTTGAAAAATTT
131 TGATGATGATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTT-AAAAA-TT
*
397370 ATTGACTTTTAAAATTAATTATTTAAAAATATAAAAAAATATTAAAATAAACTTTTAATTACAAT
194 ATTGACTTTTAAAATTAATTGTTTAAAAATAT-AAAAAATATTAAAATAAACTTTTAATTACAAT
* *
397435 TGAGGGATCAAATGAATTATTATTCATTAATTATTATTTATAACAACAATTAATAATTTTTATTC
258 TGAGGGATCAAATGAATTATTATTCATTAATTATTATTTTTAACAACAATTAATAATATTTATTC
*
397500 ATTTTTACTAAAATT
323 ATTTTTAATAAAATT
* *
397515 ATTTTGATTTTTGCATGAAATTACACAATACGTATAATCTAGTATAGGAAAACTTTAAGGGTAAA
1 ATTTTGATTTTTGCATGAAATTACACAATACATATAATCTAGTATAGGAAAACTTTGAGGGTAAA
397580 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTCTTTTACAAAATAATGAT
66 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTCTTTTAC--AATAATGAT
397645 GATGATGATGATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTAAAAATG
129 GATGATGATGATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTAAAAAT-
397710 TATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAATATT-AAATAAACTTTTAATTACAAT
193 TATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAAT
397774 TGAGGGATCAAATGAATTATTATTCATTAATTATTATTTTTAACAACAATTAATAATATTTATTC
258 TGAGGGATCAAATGAATTATTATTCATTAATTATTATTTTTAACAACAATTAATAATATTTATTC
*
397839 ATTTTTAATACAATT
323 ATTTTTAATAAAATT
* * * *
397854 ATTTTGATTTTTGCATGATATTACACAATACTTATAATTTAGTATAGGAAAACTTTGAGGGTAAG
1 ATTTTGATTTTTGCATGAAATTACACAATACATATAATCTAGTATAGGAAAACTTTGAGGGTAAA
* * *
397919 TATTTTAAAATATAAATAATTTTATAAAAGTTTTATAATTAGTATTTCGTTTACAA-AATGATGA
66 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTCTTTTACAATAATGATGA
* *
397983 TTATGATAATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATATTTTTAAAAACT
131 TGATGATGATAATAAATATTTTATAATTTAAAAAATTATAAATTTC--ATATATTTTTAAAAA-T
*
398048 TATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAATATTAAAATAATCTTTTAATTACAAT
193 TATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAAT
* * * * * *
398113 TGAGAGATCAAATGAATTATTATTCATTAATTTTTAATTTTTAATAATAGTTAATAATGTTTATT
258 TGAGGGATCAAATGAATTATTATTCATTAATTATT-ATTTTTAACAACAATTAATAATATTTATT
398178 CATTTTTAATAAAATT
322 CATTTTTAATAAAATT
398194 A
1 A
398195 GAATTTTAAA
Statistics
Matches: 633, Mismatches: 31, Indels: 24
0.92 0.05 0.03
Matches are distributed among these distances:
332 112 0.18
336 52 0.08
337 6 0.01
338 58 0.09
339 263 0.42
340 52 0.08
341 62 0.10
342 28 0.04
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (337 bp):
ATTTTGATTTTTGCATGAAATTACACAATACATATAATCTAGTATAGGAAAACTTTGAGGGTAAA
TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTCTTTTACAATAATGATGA
TGATGATGATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTAAAAATTAT
TGACTTTTAAAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAATTGA
GGGATCAAATGAATTATTATTCATTAATTATTATTTTTAACAACAATTAATAATATTTATTCATT
TTTAATAAAATT
Found at i:400962 original size:103 final size:103
Alignment explanation
Indices: 400751--400963 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
400741 GCGGTCTTTC
* * *
400751 TGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCA
1 TGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCA
*
400816 TATGTATATGATTCTTAAGGAATGATATGTGGTCCTTC
66 TATGTATATGATTCTTAAGGAATGATATGTGGTCCTTA
* *
400854 GGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGTA
1 TGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCA
400919 TATGTATATGATTCTTAAGGAATGATATGTGGTCCTTA
66 TATGTATATGATTCTTAAGGAATGATATGTGGTCCTTA
400957 TGGACAT
1 TGGACAT
400964 TATTATATGG
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (103 bp):
TGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCA
TATGTATATGATTCTTAAGGAATGATATGTGGTCCTTA
Found at i:400998 original size:23 final size:23
Alignment explanation
Indices: 400972--401039 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
400962 ATTATTATAT
* *
400972 GGCACTACGGTGTAATTCTATGC
1 GGCACTACGGTGCAATTCTACGC
* *
400995 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
401018 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
401040 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:402329 original size:25 final size:23
Alignment explanation
Indices: 402293--402339 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
402283 GTATACAATA
402293 AAATAACAAAAAACTATATTAAAAT
1 AAATAAC-AAAAACT-TATTAAAAT
402318 AAATAGAC-AAAACTTATTAAAA
1 AAATA-ACAAAAACTTATTAAAA
402340 CTATACTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 8 0.38
24 6 0.29
25 5 0.24
26 2 0.10
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (23 bp):
AAATAACAAAAACTTATTAAAAT
Found at i:406129 original size:30 final size:31
Alignment explanation
Indices: 406066--406130 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
406056 TTTATTTTAT
* * **
406066 TTTAGGGACTAAATTGAAAATTTTGGTTAAA
1 TTTAAGGACTAAAATGAAAATTTAAGTTAAA
*
406097 TTTAAGGACTAAAATGAATATTTAAG-TAAA
1 TTTAAGGACTAAAATGAAAATTTAAGTTAAA
406127 TTTA
1 TTTA
406131 GTTCTAATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.38
Consensus pattern (31 bp):
TTTAAGGACTAAAATGAAAATTTAAGTTAAA
Found at i:410335 original size:7 final size:7
Alignment explanation
Indices: 410323--410356 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
410313 GGTATGTCGC
410323 TAGTGGG
1 TAGTGGG
410330 TAGTGGG
1 TAGTGGG
410337 TAGTGGG
1 TAGTGGG
410344 TAGTGGG
1 TAGTGGG
410351 T-GTGGG
1 TAGTGGG
410357 GATGGATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.12, C:0.00, G:0.59, T:0.29
Consensus pattern (7 bp):
TAGTGGG
Found at i:411930 original size:15 final size:15
Alignment explanation
Indices: 411893--411929 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
411883 ATAATAAATA
411893 ATTAT-AAATATATT
1 ATTATAAAATATATT
411907 ATTATAAAATATATT
1 ATTATAAAATATATT
411922 ATT-TAAAA
1 ATTATAAAA
411930 AAAATTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTATAAAATATATT
Done.