Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold113
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: 3764034
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 4009 characters in sequence are not A, C, G, or T
File 18 of 23
Found at i:2726052 original size:79 final size:78
Alignment explanation
Indices: 2725957--2726361 Score: 389
Period size: 79 Copynumber: 5.2 Consensus size: 78
2725947 TTTTCGTCTT
* * * * *
2725957 AGGGGATACTCTAACCTCGCTTTTGTTTCCCAAATATTAAATCTTTTATCTTGGGGATACTCCAA
1 AGGGGATACTCCAACCTCGTTTTTATTTCCAAAATATTAAAT-TTTTATCTCGGGGATACTCCAA
***
2726022 CCTTGTT-TTTTCTA
65 CCCCATTATTTTC-A
* * * *
2726036 AGGAGATACTCCAACCTCATTTTTATTTCCAAAATATTAAAATTTTCATCTTGGGGATACTCCAA
1 AGGGGATACTCCAACCTCGTTTTTATTTCCAAAATATT-AAATTTTTATCTCGGGGATACTCCAA
* * *
2726101 CCCCATCAATTCCA
65 CCCCATTATTTTCA
* * *
2726115 AGGGGATACTCCAA-CTCGTTTTTATTTTCAAAACAGTAAA-TTTT-TCTCGAGGG-TACTCCAA
1 AGGGGATACTCCAACCTCGTTTTTATTTCCAAAATATTAAATTTTTATCTCG-GGGATACTCCAA
*
2726176 CCCTATTATTTTCGA
65 CCCCATTATTTTC-A
* * *
2726191 A-GGGATACTCCAACCCCATTTTTATTTCCAAAA-ATATCAATTTTTCATCTCGGGGATACTCCA
1 AGGGGATACTCCAACCTCGTTTTTATTTCCAAAATAT-TAAATTTTT-ATCTCGGGGATACTCCA
*
2726254 ACCCCGTTATTTTCA
64 ACCCCATTATTTTCA
* * *
2726269 AGGGGATACTCCAACC-CTGTTTTCATTTCAAAAATATTAAATTTTTAATCTCAGGGATACTCCA
1 AGGGGATACTCCAACCTC-GTTTTTATTTCCAAAATATTAAATTTTT-ATCTCGGGGATACTCCA
* * *
2726333 ACCTCA-TA-TTCCG
64 ACCCCATTATTTTCA
*
2726346 AGGGGACACTCCAACC
1 AGGGGATACTCCAACC
2726362 CTGCCTCTTT
Statistics
Matches: 271, Mismatches: 42, Indels: 28
0.79 0.12 0.08
Matches are distributed among these distances:
75 34 0.13
76 27 0.10
77 25 0.09
78 27 0.10
79 149 0.55
80 9 0.03
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (78 bp):
AGGGGATACTCCAACCTCGTTTTTATTTCCAAAATATTAAATTTTTATCTCGGGGATACTCCAAC
CCCATTATTTTCA
Found at i:2726298 original size:154 final size:154
Alignment explanation
Indices: 2726014--2726301 Score: 411
Period size: 154 Copynumber: 1.9 Consensus size: 154
2726004 ATCTTGGGGA
* * * *
2726014 TACTCCAACCTTGTTTTTTCTAAGGAGATACTCCAACCTCATTTTTATTTCCAAAATATTAAAAT
1 TACTCCAACCCTATTTTTTCGAAGGAGATACTCCAACCCCATTTTTATTTCCAAAATATTAAAAT
* * *
2726079 TTTCATCTTGGGGATACTCCAACCCCATCAATTCCAAGGGGATACTCCAACTCGTTTTTATTTTC
66 TTTCATCTCGGGGATACTCCAACCCCATCAATTCCAAGGGGATACTCCAACCCGTTTTCATTTTC
2726144 AAAACAGTAAATTTTTCTCGAGGG
131 AAAACAGTAAATTTTTCTCGAGGG
*
2726168 TACTCCAACCCTATTATTTTCGAAGG-GATACTCCAACCCCATTTTTATTTCCAAAA-ATATCAA
1 TACTCCAACCCTATT-TTTTCGAAGGAGATACTCCAACCCCATTTTTATTTCCAAAATAT-TAAA
* * * * *
2726231 TTTTTCATCTCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCTGTTTTCA-T
64 ATTTTCATCTCGGGGATACTCCAACCCCATCAATTCCAAGGGGATACTCCAACCC-GTTTTCATT
2726295 TTCAAAA
128 TTCAAAA
2726302 ATATTAAATT
Statistics
Matches: 118, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
153 2 0.02
154 101 0.86
155 15 0.13
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (154 bp):
TACTCCAACCCTATTTTTTCGAAGGAGATACTCCAACCCCATTTTTATTTCCAAAATATTAAAAT
TTTCATCTCGGGGATACTCCAACCCCATCAATTCCAAGGGGATACTCCAACCCGTTTTCATTTTC
AAAACAGTAAATTTTTCTCGAGGG
Found at i:2728041 original size:92 final size:92
Alignment explanation
Indices: 2727896--2728178 Score: 291
Period size: 92 Copynumber: 3.0 Consensus size: 92
2727886 TTTGTCTTAT
* * * * * * * *
2727896 TCTATATAGTATGACATTTATAATCAATCAAC-CTTTTACTCTTTGTGCTAAAAGAAAATCGATT
1 TCTATATAGTATGACATTTACAATCAATCAACTTTTTTTCT-TTTCTACAAAAAGAAATTTGATT
* * *
2727960 TTAAAAAATAATCGATACATTAGTTTAA
65 TTAAAAAATAATCAATGCATTAGTCTAA
* * * *
2727988 TCCT-TATAGTTTGACATTTACAATCAATCAGCTTTTTTTCTTTTCTACAAAAAGGAATTTAATT
1 T-CTATATAGTATGACATTTACAATCAATCAACTTTTTTTCTTTTCTACAAAAAGAAATTTGATT
*
2728052 TTCAAAAATAATCAATGCATTAGTCTAA
65 TTAAAAAATAATCAATGCATTAGTCTAA
** *
2728080 TCTATATAGCCTGATATTTATAATCAATCAACTCAACTTTTTTTTCTTTTCTACAAAAAGAAATT
1 TCTATATAGTATGACA-TT-T-A-CAATCAA-TCAAC-TTTTTTTCTTTTCTACAAAAAGAAATT
* *
2728145 TGATTTAAAAAAATAATCCATGCATTAGTCTAA
60 TGATTTTAAAAAATAATCAATGCATTAGTCTAA
2728178 T
1 T
2728179 ATTTGCAGTC
Statistics
Matches: 157, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
91 2 0.01
92 76 0.48
93 10 0.06
94 1 0.01
95 1 0.01
96 7 0.04
97 4 0.03
98 56 0.36
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (92 bp):
TCTATATAGTATGACATTTACAATCAATCAACTTTTTTTCTTTTCTACAAAAAGAAATTTGATTT
TAAAAAATAATCAATGCATTAGTCTAA
Found at i:2732070 original size:21 final size:21
Alignment explanation
Indices: 2732046--2732086 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2732036 TAATACCCTT
*
2732046 GAAAAGAAAGTAAATGAGTTG
1 GAAAAGAAAATAAATGAGTTG
*
2732067 GAAAAGAAAATAAGTGAGTT
1 GAAAAGAAAATAAATGAGTT
2732087 ACAAAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.20
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAGTTG
Found at i:2732092 original size:21 final size:20
Alignment explanation
Indices: 2732047--2732108 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
2732037 AATACCCTTG
* **
2732047 AAAAGAAAGTAAATGAGTTGG
1 AAAAGAAAAT-AATGAGTTAC
2732068 AAAAGAAAATAAGTGAGTTAC
1 AAAAGAAAATAA-TGAGTTAC
*
2732089 AAAATGAAAATGATGAGTTA
1 AAAA-GAAAATAATGAGTTA
2732109 ACTAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.06
21 26 0.74
22 7 0.20
ACGTcount: A:0.55, C:0.02, G:0.23, T:0.21
Consensus pattern (20 bp):
AAAAGAAAATAATGAGTTAC
Found at i:2738276 original size:13 final size:13
Alignment explanation
Indices: 2738258--2738282 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2738248 CAAAGATCAG
2738258 TGTATCGATACAA
1 TGTATCGATACAA
2738271 TGTATCGATACA
1 TGTATCGATACA
2738283 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2738360 original size:33 final size:33
Alignment explanation
Indices: 2738323--2738389 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2738313 AGTAGCTTAA
2738323 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2738356 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2738389 A
1 A
2738390 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2738363 original size:13 final size:13
Alignment explanation
Indices: 2738345--2738369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2738335 CAAAAAAATA
2738345 TGTATCGATACAT
1 TGTATCGATACAT
2738358 TGTATCGATACA
1 TGTATCGATACA
2738370 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2739015 original size:19 final size:20
Alignment explanation
Indices: 2738972--2739022 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2738962 CACACCCAGA
* *
2738972 TGTATCGATACATATTTCTT
1 TGTATCGATACATAGTTCAT
2738992 TGTATCGATACAT-GTTCAT
1 TGTATCGATACATAGTTCAT
2739011 TGTATCGATACA
1 TGTATCGATACA
2739023 CCATGAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATAGTTCAT
Found at i:2739128 original size:20 final size:19
Alignment explanation
Indices: 2739099--2739139 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
2739089 AGCTCAATGG
*
2739099 TTATAATTGTATCGATACA
1 TTATAATTGTATCAATACA
2739118 TTATGAATTGTATCAATACA
1 TTAT-AATTGTATCAATACA
2739138 TT
1 TT
2739140 GAGCCTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (19 bp):
TTATAATTGTATCAATACA
Found at i:2743073 original size:2 final size:2
Alignment explanation
Indices: 2743066--2743100 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2743056 AAATTGACAT
2743066 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2743101 GAGAAATGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2752723 original size:133 final size:134
Alignment explanation
Indices: 2752509--2752763 Score: 356
Period size: 133 Copynumber: 1.9 Consensus size: 134
2752499 CACCATAGTT
* * *
2752509 AAAGTCCACATGAGTTGGTGGCATCCCATTCAAAGTTCACACAAGTTCATGGCAACAAAACCTTT
1 AAAGTCCACAAGAGTTGGTGGCACCCCAATCAAAGTTCACACAAGTTCATGGCAACAAAACCTTT
*
2752574 TCAAAGTCCATACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAACCAAACAT
66 TCAAAGTCCACACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAACCAAACAT
2752639 TTTC
131 TTTC
* *
2752643 AAAGTCCACAAGAGTTGGTGGACACCCCAATCAAA-TTCCACATAAG-TCAGTGGC-AC-AATCC
1 AAAGTCCACAAGAGTTGGTGG-CACCCCAATCAAAGTT-CACACAAGTTCA-TGGCAACAAAACC
* * * * *
2752704 TTTTTAAAGTCCACACGAGTTGGTGGTACCCTAGTTAAAGTCCACACGAGTTGGTGGCAA
63 TTTTCAAAGTCCACACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAA
2752764 ACTTTTCAAT
Statistics
Matches: 107, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
133 58 0.54
134 27 0.25
135 22 0.21
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (134 bp):
AAAGTCCACAAGAGTTGGTGGCACCCCAATCAAAGTTCACACAAGTTCATGGCAACAAAACCTTT
TCAAAGTCCACACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAACCAAACAT
TTTC
Found at i:2752725 original size:66 final size:66
Alignment explanation
Indices: 2752509--2752791 Score: 240
Period size: 67 Copynumber: 4.3 Consensus size: 66
2752499 CACCATAGTT
* * *
2752509 AAAGTCCACATGAGTTGGTGGCATCCCATTCAAAGTT-CACACAAGTTCA-TGGCAACAAAACCT
1 AAAGTCCACACGAGTTGGTGGCACCCCAATCAAA-TTCCACACAAG-TCAGTGGCAAC-AAACCT
2752572 TTTC
63 TTTC
* * * * * * *
2752576 AAAGTCCATACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGT-TGATGGCAACCAAACATT
1 AAAGTCCACACGAGTTGGTGGCACCCCAATCAAATTCCACACAAGTCAG-TGGCAA-CAAACCTT
2752640 TTC
64 TTC
* * *
2752643 AAAGTCCACAAGAGTTGGTGGACACCCCAATCAAATTCCACATAAGTCAGTGGC-ACAATCCTTT
1 AAAGTCCACACGAGTTGGTGG-CACCCCAATCAAATTCCACACAAGTCAGTGGCAACAAACCTTT
*
2752707 TT
65 TC
* * * * * * **
2752709 AAAGTCCACACGAGTTGGTGGTACCCTAGTTAAAGTCCACACGAGTTGGTGG---CAAA-CTTTT
1 AAAGTCCACACGAGTTGGTGGCACCCCAATCAAATTCCACACAAGTCAGTGGCAACAAACCTTTT
2752770 C
66 C
* *
2752771 AATGTCCACACGAGTTAGTGG
1 AAAGTCCACACGAGTTGGTGG
2752792 TACCAAAGTT
Statistics
Matches: 176, Mismatches: 34, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
62 24 0.14
63 3 0.02
65 22 0.12
66 30 0.17
67 71 0.40
68 25 0.14
69 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (66 bp):
AAAGTCCACACGAGTTGGTGGCACCCCAATCAAATTCCACACAAGTCAGTGGCAACAAACCTTTT
C
Found at i:2752916 original size:293 final size:289
Alignment explanation
Indices: 2752393--2753151 Score: 795
Period size: 293 Copynumber: 2.6 Consensus size: 289
2752383 TTTAATGTCT
* * * *
2752393 ACATAAGTTGGTGGCACAATCCTTTTCAAAGTCCACAC----TAGTGGCACCCTAGTCAAAGTCC
1 ACATAAGTTAGTGGCACAATCCTTTTTAAAGTCCACACGAGTTGGTGGCACCCTAGTTAAAGTCC
* * * * * * *
2752454 ACACAAGTTAGTGACAACCTTTTCAAGGTCCAAATG-GCTTGGTGGCACCATAGTTAAAGTCCAC
66 ACACAAGTTGGTGGCAAACTTTTCAAAGTCCACACGAG-TTGGTGGCACCAAAGTTAAAGTCCAC
** *
2752518 ATGAGTTGGTGGCATCCC-ATTCAAAGTTCACACAAGTTCATGGCAACAAAACCTTTTCAAAGTC
130 ATGAGTTGGTGGCA-CCCTATTCAAAG-TCACACAAGTTGGTGGCAACCAAACCTTTTCAAAGTC
* *
2752582 CATACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAACCAAACATTTTCAAAG
193 CATAC-AGTTGGTGGCACCCTAGTAAAAGTCAACACAAGTTGAT-CCAACCAAACATTTTCAAAG
* * *
2752647 TCCACAAGAGTTGGTGGACACCCCAATCAAATTCC
256 TCCACAAGAGCTGGTGG-CACCACAATCAAAGTCC
* *
2752682 ACATAAGTCAGTGGCACAATCCTTTTTAAAGTCCACACGAGTTGGTGGTACCCTAGTTAAAGTCC
1 ACATAAGTTAGTGGCACAATCCTTTTTAAAGTCCACACGAGTTGGTGGCACCCTAGTTAAAGTCC
* * * *
2752747 ACACGAGTTGGTGGCAAACTTTTCAATGTCCACACGAGTTAGTGGTACCAAAGTTAAAGTCCACA
66 ACACAAGTTGGTGGCAAACTTTTCAAAGTCCACACGAGTTGGTGGCACCAAAGTTAAAGTCCACA
* *
2752812 CGAGTTGGTGGCACCCTATTCAAAGTCGACACAAGTTGGTGGCAACCAAACCTTTTTAAAGTCTA
131 TGAGTTGGTGGCACCCTATTCAAAGTC-ACACAAGTTGGTGGCAACCAAACCTTTTCAAAGTC--
* * * * *
2752877 CATA-ATTTGGTGGTACCCTAGTCAAAGTCAACACAAGTTGGTCCAACCAAACCTTTTCAAAGTC
193 CATACAGTTGGTGGCACCCTAGTAAAAGTCAACACAAGTTGATCCAACCAAACATTTTCAAAGTC
* *
2752941 CACACGAGCTGGTGGCACCATAATCAAAGTCC
258 CACAAGAGCTGGTGGCACCACAATCAAAGTCC
** * * ** * * *
2752973 ACATGTGTTTA-TGGTAC---CATAGTTAAAGTCCACATGAGTTGGTAGCACCTTA-TTCAAAGT
1 ACATAAG-TTAGTGGCACAATCCTTTTTAAAGTCCACACGAGTTGGTGGCACCCTAGTT-AAAGT
* * ** * *
2753033 CCACACAAGTCGATGGCAACCAAACCTTTTCAAAGTCCACACGAGTTGGTGGCACCCCAGTCAAT
64 CCACACAAGTTGGTGG----CAAA-CTTTTCAAAGTCCACACGAGTTGGTGGCACCAAAGTTAAA
* * ** *
2753098 GTCCACATGAGTTAGTGGCACCCTAGTCAAAGTCTACATGAGTTGGTGACAACC
124 GTCCACATGAGTTGGTGGCACCCTATTCAAAGTC-ACACAAGTTGGTGGCAACC
2753152 TTTTCGAAGT
Statistics
Matches: 393, Mismatches: 61, Indels: 28
0.82 0.13 0.06
Matches are distributed among these distances:
287 2 0.01
288 46 0.12
289 35 0.09
291 24 0.06
292 44 0.11
293 237 0.60
294 1 0.00
295 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (289 bp):
ACATAAGTTAGTGGCACAATCCTTTTTAAAGTCCACACGAGTTGGTGGCACCCTAGTTAAAGTCC
ACACAAGTTGGTGGCAAACTTTTCAAAGTCCACACGAGTTGGTGGCACCAAAGTTAAAGTCCACA
TGAGTTGGTGGCACCCTATTCAAAGTCACACAAGTTGGTGGCAACCAAACCTTTTCAAAGTCCAT
ACAGTTGGTGGCACCCTAGTAAAAGTCAACACAAGTTGATCCAACCAAACATTTTCAAAGTCCAC
AAGAGCTGGTGGCACCACAATCAAAGTCC
Found at i:2752941 original size:195 final size:195
Alignment explanation
Indices: 2752740--2753096 Score: 493
Period size: 195 Copynumber: 1.8 Consensus size: 195
2752730 TACCCTAGTT
* ** *
2752740 AAAGTCCACACGAGTTGGTGGCAA-ACTTTTCAATGTCCACACGAG-TTAGTGGTACCAAAGTTA
1 AAAGTCCACACGAGCTGGTGGCAACA-TAATCAAAGTCCACACGAGTTTA-TGGTACCAAAGTTA
* * * *
2752803 AAGTCCACACGAGTTGGTGGCACCCTATTCAAAGTCGACACAAGTTGGTGGCAACCAAACCTTTT
64 AAGTCCACACGAGTTGGTAGCACCCTATTCAAAGTCCACACAAGTCGATGGCAACCAAACCTTTT
* * * * * *
2752868 TAAAGTCTACATAATTTGGTGGTACCCTAGTCAAAGTCAACACAAGTTGGTCCAACCAAACCTTT
129 CAAAGTCCACACAAGTTGGTGGCACCCCAGTCAAAGTCAACACAAGTTGGTCCAACCAAACCTTT
2752933 TC
194 TC
* * * *
2752935 AAAGTCCACACGAGCTGGTGGCACCATAATCAAAGTCCACATGTGTTTATGGTACCATAGTTAAA
1 AAAGTCCACACGAGCTGGTGGCAACATAATCAAAGTCCACACGAGTTTATGGTACCAAAGTTAAA
* *
2753000 GTCCACATGAGTTGGTAGCACCTTATTCAAAGTCCACACAAGTCGATGGCAACCAAACCTTTTCA
66 GTCCACACGAGTTGGTAGCACCCTATTCAAAGTCCACACAAGTCGATGGCAACCAAACCTTTTCA
*
2753065 AAGTCCACACGAGTTGGTGGCACCCCAGTCAA
131 AAGTCCACACAAGTTGGTGGCACCCCAGTCAA
2753097 TGTCCACATG
Statistics
Matches: 139, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
195 135 0.97
196 4 0.03
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (195 bp):
AAAGTCCACACGAGCTGGTGGCAACATAATCAAAGTCCACACGAGTTTATGGTACCAAAGTTAAA
GTCCACACGAGTTGGTAGCACCCTATTCAAAGTCCACACAAGTCGATGGCAACCAAACCTTTTCA
AAGTCCACACAAGTTGGTGGCACCCCAGTCAAAGTCAACACAAGTTGGTCCAACCAAACCTTTTC
Found at i:2753006 original size:226 final size:226
Alignment explanation
Indices: 2752445--2752975 Score: 502
Period size: 226 Copynumber: 2.3 Consensus size: 226
2752435 GGCACCCTAG
* * * * *
2752445 TCAAAGTCCACACAAGTTAGTG--AC-AACCTTTTCAAGGTCCAAATG-GCTTGGTGGCACCATA
1 TCAAAGTCAACACAAGTCAGTGCCACAAACCTTTTCAAAGTCCACACGAGC-TGGTGGCACCATA
* * * * ** ** * * * *
2752506 GTTAAAGTCCACATGAGTTGGTGGCATCCCATTCAAAGTTCACACAAGTTCA-TGGCAACAAAAC
65 ATCAAAGTCCACACGAGTTGATGGCAAACTGTTCAAAGTCCACACGAGTT-AGTGG-TACCAAA-
* *
2752570 CTTTTCAAAGTCCATACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAACCAA
127 --GTT-AAAGTCCACACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAACCAA
2752635 ACATTTTCAAAGTCCACAAGAGTTGGTGGACACCCCAA
189 ACATTTTCAAAGTCCACAAGAGTTGGTGGACACCCCAA
* * * * * * * * * *
2752673 TCAAATTCCACATAAGTCAGTGGCACAATCCTTTTTAAAGTCCACACGAGTTGGTGGTACCCTAG
1 TCAAAGTCAACACAAGTCAGTGCCACAAACCTTTTCAAAGTCCACACGAGCTGGTGGCACCATAA
* * * *
2752738 TTAAAGTCCACACGAGTTGGTGGCAAACTTTTCAATGTCCACACGAGTTAGTGGTACCAAAGTTA
66 TCAAAGTCCACACGAGTTGATGGCAAACTGTTCAAAGTCCACACGAGTTAGTGGTACCAAAGTTA
* * * * *
2752803 AAGTCCACACGAGTTGGTGGCACCCTATTCAAAGTCGACACAAGTTGGTGGCAACCAAACCTTTT
131 AAGTCCACACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAACCAAACATTTT
* * * * * *
2752868 TAAAGTCTACATA-ATTTGGTGG-TACCCTAG
196 CAAAGTCCACA-AGAGTTGGTGGACACCCCAA
**
2752898 TCAAAGTCAACACAAGTTGGT-CCAACCAAACCTTTTCAAAGTCCACACGAGCTGGTGGCACCAT
1 TCAAAGTCAACACAAGTCAGTGCC-A-CAAACCTTTTCAAAGTCCACACGAGCTGGTGGCACCAT
2752962 AATCAAAGTCCACA
64 AATCAAAGTCCACA
2752976 TGTGTTTATG
Statistics
Matches: 248, Mismatches: 47, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
224 1 0.00
225 22 0.09
226 122 0.49
227 3 0.01
228 19 0.08
230 8 0.03
231 72 0.29
232 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (226 bp):
TCAAAGTCAACACAAGTCAGTGCCACAAACCTTTTCAAAGTCCACACGAGCTGGTGGCACCATAA
TCAAAGTCCACACGAGTTGATGGCAAACTGTTCAAAGTCCACACGAGTTAGTGGTACCAAAGTTA
AAGTCCACACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAACCAAACATTTT
CAAAGTCCACAAGAGTTGGTGGACACCCCAA
Found at i:2753034 original size:226 final size:226
Alignment explanation
Indices: 2752445--2753038 Score: 490
Period size: 226 Copynumber: 2.6 Consensus size: 226
2752435 GGCACCCTAG
* * * * *
2752445 TCAAAGTCCACACAAGTTAGTG--AC-AACCTTTTCAAGGTCCAAATG-GCTTGGTGGCACCATA
1 TCAAAGTCAACACAAGTCAGTGCCACAAACCTTTTCAAAGTCCACACGAGC-TGGTGGCACCATA
* * * * ** ** * * * *
2752506 GTTAAAGTCCACATGAGTTGGTGGCATCCCATTCAAAGTTCACACAAGTTCATGGCAACAAAACC
65 ATCAAAGTCCACACGAGTTGATGGCAAACTGTTCAAAGTCCACACGAGTT-A--GTAGC---ACC
*
2752571 TT-TTCAAAGTCCATACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAACCAA
124 TTATTCAAAGTCCACACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAACCAA
2752635 ACATTTTCAAAGTCCACAAGAGTTGGTGGACACCCCAA
189 ACATTTTCAAAGTCCACAAGAGTTGGTGGACACCCCAA
* * * * * * * * * *
2752673 TCAAATTCCACATAAGTCAGTGGCACAATCCTTTTTAAAGTCCACACGAGTTGGTGGTACCCTAG
1 TCAAAGTCAACACAAGTCAGTGCCACAAACCTTTTCAAAGTCCACACGAGCTGGTGGCACCATAA
* * * * * * **
2752738 TTAAAGTCCACACGAGTTGGTGGCAAACTTTTCAATGTCCACACGAGTTAGTGGTACCAAAGTT-
66 TCAAAGTCCACACGAGTTGATGGCAAACTGTTCAAAGTCCACACGAGTTAGTAGCACCTTA-TTC
* * * * *
2752802 AAAGTCCACACGAGTTGGTGGCACCCTATTCAAAGTCGACACAAGTTGGTGGCAACCAAACCTTT
130 AAAGTCCACACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAACCAAACATTT
* * * * * *
2752867 TTAAAGTCTACATA-ATTTGGTGG-TACCCTAG
195 TCAAAGTCCACA-AGAGTTGGTGGACACCCCAA
**
2752898 TCAAAGTCAACACAAGTTGGT-CCAACCAAACCTTTTCAAAGTCCACACGAGCTGGTGGCACCAT
1 TCAAAGTCAACACAAGTCAGTGCC-A-CAAACCTTTTCAAAGTCCACACGAGCTGGTGGCACCAT
* * * * * * *
2752962 AATCAAAGTCCACATGTGTTTATGG-TACCATAGTT-AAAGTCCACATGAGTTGGTAGCACCTTA
64 AATCAAAGTCCACACGAGTTGATGGCAAAC-T-GTTCAAAGTCCACACGAGTTAGTAGCACCTTA
2753025 TTCAAAGTCCACAC
127 TTCAAAGTCCACAC
2753039 AAGTCGATGG
Statistics
Matches: 290, Mismatches: 64, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
224 1 0.00
225 29 0.10
226 162 0.56
227 5 0.02
228 20 0.07
230 3 0.01
231 69 0.24
232 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (226 bp):
TCAAAGTCAACACAAGTCAGTGCCACAAACCTTTTCAAAGTCCACACGAGCTGGTGGCACCATAA
TCAAAGTCCACACGAGTTGATGGCAAACTGTTCAAAGTCCACACGAGTTAGTAGCACCTTATTCA
AAGTCCACACGAGTTGGTGGCACCCTAGTAAAAGTCCACACAAGTTGATGGCAACCAAACATTTT
CAAAGTCCACAAGAGTTGGTGGACACCCCAA
Found at i:2753083 original size:129 final size:128
Alignment explanation
Indices: 2752898--2753167 Score: 348
Period size: 129 Copynumber: 2.1 Consensus size: 128
2752888 GGTACCCTAG
* * * *
2752898 TCAAAGTCAACACAAGTTGGTCCAACCAAACCTTTTCAAAGTCCACACGAGCTGGTGGCACCATA
1 TCAAAGTCCACACAAGTCGATCCAACCAAACCTTTTCAAAGTCCACACGAGCTGGTGGCACCACA
* * *
2752963 ATCAAAGTCCACATGTGTTTA-TGGTACCATAGTTAAAGTCCACATGAGTTGGT-AGC-ACCTTA
66 ATCAAAGTCCACATGAG-TTAGTGGCACCATAGTCAAAGTCCACATGAGTTGGTGA-CAACCTT-
2753025 T
128 T
* * *
2753026 TCAAAGTCCACACAAGTCGATGGCAACCAAACCTTTTCAAAGTCCACACGAGTTGGTGGCACCCC
1 TCAAAGTCCACACAAGTCGAT-CCAACCAAACCTTTTCAAAGTCCACACGAGCTGGTGGCACCAC
* * * *
2753091 AGTCAATGTCCACATGAGTTAGTGGCACCCTAGTCAAAGTCTACATGAGTTGGTGACAACCTTT
65 AATCAAAGTCCACATGAGTTAGTGGCACCATAGTCAAAGTCCACATGAGTTGGTGACAACCTTT
*
2753155 TCGAAGTCCACAC
1 TCAAAGTCCACAC
2753168 GAGTTGGTGG
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
128 21 0.17
129 96 0.78
130 6 0.05
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (128 bp):
TCAAAGTCCACACAAGTCGATCCAACCAAACCTTTTCAAAGTCCACACGAGCTGGTGGCACCACA
ATCAAAGTCCACATGAGTTAGTGGCACCATAGTCAAAGTCCACATGAGTTGGTGACAACCTTT
Found at i:2753151 original size:98 final size:93
Alignment explanation
Indices: 2753000--2753177 Score: 221
Period size: 98 Copynumber: 1.9 Consensus size: 93
2752990 CATAGTTAAA
* * *
2753000 GTCCACATGAGTTGGTAGCACCTTATTCAAAGTCCACACAAGTCGATGGCAACCAAACCTTTTCA
1 GTCCACATGAGTTAGTAGCACCCTAGTCAAAGTCCACACAAGTCGAT-G--A-C-AACCTTTTCA
2753065 AAGTCCACACGAGTTGGTGGCACCCCAGTCAAT
61 AAGTCCACACGAGTTGGTGGCACCCCAGTCAAT
* * ** * * *
2753098 GTCCACATGAGTTAGTGGCACCCTAGTCAAAGTCTACATGAGTTGGTGACAACCTTTTCGAAGTC
1 GTCCACATGAGTTAGTAGCACCCTAGTCAAAGTCCACACAAGTCGATGACAACCTTTTCAAAGTC
2753163 CACACGAGTTGGTGG
66 CACACGAGTTGGTGG
2753178 TAACCTTTTC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
93 29 0.41
94 1 0.01
95 1 0.01
97 1 0.01
98 38 0.54
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (93 bp):
GTCCACATGAGTTAGTAGCACCCTAGTCAAAGTCCACACAAGTCGATGACAACCTTTTCAAAGTC
CACACGAGTTGGTGGCACCCCAGTCAAT
Found at i:2753183 original size:31 final size:31
Alignment explanation
Indices: 2752398--2753219 Score: 294
Period size: 31 Copynumber: 25.7 Consensus size: 31
2752388 TGTCTACATA
2752398 AGTTGGTGGCACAATCCTTTTCAAAGTCCACAC-
1 AGTTGGTGG--CAA-CCTTTTCAAAGTCCACACG
* * ** *
2752431 ---TAGTGGCACCCTAGTCAAAGTCCACACA
1 AGTTGGTGGCAACCTTTTCAAAGTCCACACG
* * * * *
2752459 AGTTAGTGACAACCTTTTCAAGGTCCAAATG
1 AGTTGGTGGCAACCTTTTCAAAGTCCACACG
* *
2752490 -GCTTGGTGGC-ACCATAGTT-AAAGTCCACATG
1 AG-TTGGTGGCAACC-T-TTTCAAAGTCCACACG
* ** * *
2752521 AGTTGGTGGCATCCCATTCAAAGTTCACACA
1 AGTTGGTGGCAACCTTTTCAAAGTCCACACG
** *
2752552 AGTTCATGGCAACAAAACCTTTTCAAAGTCCATACG
1 AGTTGGTGG---C--AACCTTTTCAAAGTCCACACG
* ** * *
2752588 AGTTGGTGGCACCCTAGTAAAAGTCCACACA
1 AGTTGGTGGCAACCTTTTCAAAGTCCACACG
* *
2752619 AGTTGATGGCAACCAAACATTTTCAAAGTCCACAAG
1 AGTTGGTGGCAA-C---C-TTTTCAAAGTCCACACG
* *** * **
2752655 AGTTGGTGGACACCCCAATCAAATTCCACATA
1 AGTTGGTGG-CAACCTTTTCAAAGTCCACACG
** *
2752687 AGTCAGTGGCACAATCCTTTTTAAAGTCCACACG
1 AGTTGGTGG--CAA-CCTTTTCAAAGTCCACACG
* * *
2752721 AGTTGGTGGTACCCTAGTT-AAAGTCCACACG
1 AGTTGGTGGCAACCT-TTTCAAAGTCCACACG
* *
2752752 AGTTGGTGGCAAACTTTTCAATGTCCACACG
1 AGTTGGTGGCAACCTTTTCAAAGTCCACACG
* * **
2752783 AGTTAGTGG-TACCAAAGTT-AAAGTCCACACG
1 AGTTGGTGGCAACC--TTTTCAAAGTCCACACG
* * * *
2752814 AGTTGGTGGCACCCTATTCAAAGTCGACACA
1 AGTTGGTGGCAACCTTTTCAAAGTCCACACG
* * **
2752845 AGTTGGTGGCAACCAAACCTTTTTAAAGTCTACATA
1 AGTTGGTGG----C-AACCTTTTCAAAGTCCACACG
* * * ** * *
2752881 ATTTGGTGGTACCCTAGTCAAAGTCAACACA
1 AGTTGGTGGCAACCTTTTCAAAGTCCACACG
**
2752912 AGTTGGTCCAACCAAACCTTTTCAAAGTCCACACG
1 AGTTGGT---GGC-AACCTTTTCAAAGTCCACACG
* ** *
2752947 AGCTGGTGGC-ACCATAATCAAAGTCCACATG
1 AGTTGGTGGCAACC-TTTTCAAAGTCCACACG
* ** * * *
2752978 TGTTTATGG-TACCATAGTT-AAAGTCCACATG
1 AGTTGGTGGCAACC-T-TTTCAAAGTCCACACG
* *
2753009 AGTTGGTAGC-ACCTTATTCAAAGTCCACACA
1 AGTTGGTGGCAACCTT-TTCAAAGTCCACACG
* *
2753040 AGTCGATGGCAACCAAACCTTTTCAAAGTCCACACG
1 AGTTGGTGG----C-AACCTTTTCAAAGTCCACACG
* *** * *
2753076 AGTTGGTGGCACCCCAGTCAATGTCCACATG
1 AGTTGGTGGCAACCTTTTCAAAGTCCACACG
* * ** * *
2753107 AGTTAGTGGCACCCTAGTCAAAGTCTACATG
1 AGTTGGTGGCAACCTTTTCAAAGTCCACACG
* *
2753138 AGTTGGTGACAACCTTTTCGAAGTCCACACG
1 AGTTGGTGGCAACCTTTTCAAAGTCCACACG
*
2753169 AGTTGGTGGTAACCTTTTCAAAG-CCTACA--
1 AGTTGGTGGCAACCTTTTCAAAGTCC-ACACG
* *
2753198 AGTTAGTGGCACCCTTTT-AAAG
1 AGTTGGTGGCAACCTTTTCAAAG
2753220 CCCATGCATA
Statistics
Matches: 580, Mismatches: 158, Indels: 107
0.69 0.19 0.13
Matches are distributed among these distances:
27 16 0.03
28 6 0.01
29 15 0.03
30 25 0.04
31 339 0.58
32 34 0.06
33 5 0.01
34 20 0.03
35 25 0.04
36 88 0.15
37 7 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (31 bp):
AGTTGGTGGCAACCTTTTCAAAGTCCACACG
Found at i:2753407 original size:29 final size:29
Alignment explanation
Indices: 2753343--2753414 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
2753333 TTTAAAGCCT
* *
2753343 ACAAGTCACTGGCACCCTTTCAAAAGTCC
1 ACAAGTTAATGGCACCCTTTCAAAAGTCC
*
2753372 ACAAGTTAGTGGCACCCTTTCAAAAGTCC
1 ACAAGTTAATGGCACCCTTTCAAAAGTCC
*
2753401 ATAAGTTAATGGCA
1 ACAAGTTAATGGCA
2753415 TCATTCCTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (29 bp):
ACAAGTTAATGGCACCCTTTCAAAAGTCC
Found at i:2760806 original size:20 final size:20
Alignment explanation
Indices: 2760781--2760820 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2760771 AAACATCAAG
2760781 ACAATCCTAAAACTACCACA
1 ACAATCCTAAAACTACCACA
2760801 ACAATCCTAAAACTACCACA
1 ACAATCCTAAAACTACCACA
2760821 TCCAAGGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (20 bp):
ACAATCCTAAAACTACCACA
Found at i:2762416 original size:29 final size:29
Alignment explanation
Indices: 2762284--2763172 Score: 1134
Period size: 29 Copynumber: 30.9 Consensus size: 29
2762274 AAAAAAAATG
*
2762284 GTGCCACTAACTCGTGTGGGCTTTGAAAAGA
1 GTGCCACTGACT--TGTGGGCTTTGAAAAGA
*
2762315 GTTGCCACTAACTCGTGTGGGCTTTG-AAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
*
2762346 GTGCCATTGACTTGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
2762374 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
2762403 GTGCCACTAACTTGTGGGCTTTG-ATAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
2762431 GTGCCACTAACTTACGTGGGCTTTGAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
*
2762462 -TGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
2762490 -TGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
2762518 GTGCCACTAACTTGTGGGCTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
2762546 GTGCCACTGATTTGTGGGCTTT-AAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
2762574 GTGCCACTGACTTGCATGGGCTTTGAAAAG-
1 GTGCCACTGACTTG--TGGGCTTTGAAAAGA
*
2762604 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
2762633 -TGCCACTAACTTGTAGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
2762660 GCGCCACTGAGTTGT--G----GAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
2762683 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
2762712 GTTGCCACCGACTCGTGTGGGCTTTGAAAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
*
2762744 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
2762772 GTGCCACTGACTTATGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
2762801 GTGCCACTGAATTGTGGGATTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
2762829 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
2762858 GTGCCACTGATTTATGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
2762887 GTGCCCACTGACTTTTGGGCTTTGAAAGGA
1 GTG-CCACTGACTTGTGGGCTTTGAAAAGA
2762917 GTGCCACTGACTTGTGGGCTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
2762945 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
2762974 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
2763003 GTGTCACTGACTTGTAGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
2763032 GTGCCACTGATTTGTGGGCTTTGAAAATA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
2763061 GTGTCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
2763090 GTGTCACTGACTTATGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
2763118 GTGCCACTGACTCGTGGACTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
2763147 GTGGCACTGACTTGTGGGCTTTGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAA
2763173 GGGATGAACA
Statistics
Matches: 761, Mismatches: 69, Indels: 58
0.86 0.08 0.07
Matches are distributed among these distances:
22 1 0.00
23 17 0.02
25 1 0.00
26 1 0.00
27 3 0.00
28 281 0.37
29 303 0.40
30 88 0.12
31 24 0.03
32 42 0.06
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:2763173 original size:57 final size:57
Alignment explanation
Indices: 2762284--2763175 Score: 1129
Period size: 57 Copynumber: 15.5 Consensus size: 57
2762274 AAAAAAAATG
* * *
2762284 GTGCCACTAACTCGTGTGGGCTTTGAAAAGAGTTGCCACTAACTCGTGTGGGCTTTG-AAAGA
1 GTGCCACTGACT--TGTGGGCTTTG-AAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAGA
* *
2762346 GTGCCATTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
2762403 GTGCCACTAACTTGTGGGCTTTGATAGGGTGCCACTAACTTACGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAAGA
* *
2762462 -TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
2762518 GTGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGATTTGTGGGCTTT-AAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
2762574 GTGCCACTGACTTGCATGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTG--TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
2762633 -TGCCACTAACTTGTAGGCTTTGAAAGGGCGCCACTGAGTTGT--G----GAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
2762683 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAGA
* *
2762744 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
2762801 GTGCCACTGAATTGTGGGATTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * * *
2762858 GTGCCACTGATTTATGGGCTTTGAAAAGAGTGCCCACTGACTTTTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTG-CCACTGACTTGTGGGCTTTGAAAAGA
* *
2762917 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
2762974 GTGCCACTGATTTGTGGGCTTTGAAAAGAGTGTCACTGACTTGTAGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* ** *
2763032 GTGCCACTGATTTGTGGGCTTTGAAAATAGTGTCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
2763090 GTGTCACTGACTTATGGGCTTTGAAAGGGTGCCACTGACTCGTGGACTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
*
2763147 GTGGCACTGACTTGTGGGCTTTGAAAGGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGGG
2763176 ATGAACATTC
Statistics
Matches: 735, Mismatches: 74, Indels: 47
0.86 0.09 0.05
Matches are distributed among these distances:
50 6 0.01
51 20 0.03
52 4 0.01
53 9 0.01
54 1 0.00
55 3 0.00
56 69 0.09
57 275 0.37
58 215 0.29
59 78 0.11
60 15 0.02
61 30 0.04
62 10 0.01
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (57 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:2778410 original size:20 final size:20
Alignment explanation
Indices: 2778381--2778457 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
2778371 GTAAAAAGAC
2778381 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
2778401 AGAATATATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
2778421 TA-CATGTATCGATATATTGA
1 -AGAATGTATCGATACATTGA
*
2778441 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
2778458 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:2780496 original size:20 final size:21
Alignment explanation
Indices: 2780457--2780508 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2780447 TTTTACAATT
*
2780457 TGTATCGATACAATAAGTGAA
1 TGTATCGATACAACAAGTGAA
*
2780478 TGTATTGATAC-ACAAGTGAA
1 TGTATCGATACAACAAGTGAA
*
2780498 TGTATCAATAC
1 TGTATCGATAC
2780509 TAAGGCTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (21 bp):
TGTATCGATACAACAAGTGAA
Found at i:2784944 original size:20 final size:21
Alignment explanation
Indices: 2784896--2784954 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
2784886 AAAAACCCAT
2784896 AATGTATCGATACAATTGTAAGC
1 AATGTATCGATAC-ATT-TAAGC
*
2784919 -ATGTATCGATACATTT-ATC
1 AATGTATCGATACATTTAAGC
2784938 AATGTATCGATACATTT
1 AATGTATCGATACATTT
2784955 CCTTGGCAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 2 0.06
20 17 0.50
21 3 0.09
22 12 0.35
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTAAGC
Found at i:2785723 original size:61 final size:61
Alignment explanation
Indices: 2785652--2785966 Score: 169
Period size: 61 Copynumber: 5.3 Consensus size: 61
2785642 GATGTGCTAG
** *
2785652 TGTGCAGATTCAAGGCCTTCAACACTAGACTTAAAGATG-ATAAGGATGA-AAAGGGTACCAA
1 TGTGCAGATTCAAGGCCAGCAACACTAGACTTAAAGATGTA-AAGAATGATAAA-GGTACCAA
* * * *
2785713 TGTGCTGATTCAAGGTCAGCAACATTAGACTTAAAGATGTAAAGAATGATAAAGGTGCCAA
1 TGTGCAGATTCAAGGCCAGCAACACTAGACTTAAAGATGTAAAGAATGATAAAGGTACCAA
** * * * * *
2785774 CATGCCGATTCAAGGCCAGCAATATTGGGCTTAAAGA--TAACA-AATG-T----G--CCAA
1 TGTGCAGATTCAAGGCCAGCAACACTAGACTTAAAGATGTAA-AGAATGATAAAGGTACCAA
* * * * * * *
2785826 TGTGCTGTTTCAAGGCTAGCAACA-TAGAACTTGAAA-ATG-ATAAGGATGA-GAAGAATGCCAA
1 TGTGCAGATTCAAGGCCAGCAACACTAG-ACTT-AAAGATGTA-AAGAATGATAAAG-GTACCAA
* * * * * * *
2785887 TGTGCTGATTCAAGGCCAACAACATTGGACTTGAAGATG-AGAAGAATGATAAAGGTGCCGA
1 TGTGCAGATTCAAGGCCAGCAACACTAGACTTAAAGATGTA-AAGAATGATAAAGGTACCAA
* *
2785948 TATGCTGATTCAAGGCCAG
1 TGTGCAGATTCAAGGCCAG
2785967 TGATGTCGAT
Statistics
Matches: 198, Mismatches: 36, Indels: 40
0.72 0.13 0.15
Matches are distributed among these distances:
51 2 0.01
52 26 0.13
53 5 0.03
54 5 0.03
58 1 0.01
59 7 0.04
60 3 0.02
61 140 0.71
62 9 0.05
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (61 bp):
TGTGCAGATTCAAGGCCAGCAACACTAGACTTAAAGATGTAAAGAATGATAAAGGTACCAA
Found at i:2785985 original size:28 final size:28
Alignment explanation
Indices: 2785945--2786003 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
2785935 ATAAAGGTGC
**
2785945 CGATATGCTGATTCAAGGCCAGTGATGT
1 CGATATGCTGATTCAAGGCCAGCAATGT
2785973 CGATATGCTGATTCAAGGCCAGCAATGT
1 CGATATGCTGATTCAAGGCCAGCAATGT
2786001 CGA
1 CGA
2786004 AGTTGAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (28 bp):
CGATATGCTGATTCAAGGCCAGCAATGT
Found at i:2786040 original size:89 final size:89
Alignment explanation
Indices: 2785889--2786054 Score: 260
Period size: 89 Copynumber: 1.9 Consensus size: 89
2785879 AATGCCAATG
* *
2785889 TGCTGATTCAAGGCCAACAACATTGGACTTGAAGATGAGAAGAATGATAAAGGTGCCGATATGCT
1 TGCTGATTCAAGGCCAACAACATCGAACTTGAAGATGAGAAGAATGATAAAGGTGCCGATATGCT
2785954 GATTCAAGGCCAGTGATGTCGATA
66 GATTCAAGGCCAGTGATGTCGATA
* ** * * *
2785978 TGCTGATTCAAGGCCAGCAATGTCGAAGTTGAAGATGAGAAGAATGATAATGGTTCCGATATGCT
1 TGCTGATTCAAGGCCAACAACATCGAACTTGAAGATGAGAAGAATGATAAAGGTGCCGATATGCT
2786043 GATTCAAGGCCA
66 GATTCAAGGCCA
2786055 ACGATATTGG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 69 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (89 bp):
TGCTGATTCAAGGCCAACAACATCGAACTTGAAGATGAGAAGAATGATAAAGGTGCCGATATGCT
GATTCAAGGCCAGTGATGTCGATA
Found at i:2786071 original size:61 final size:61
Alignment explanation
Indices: 2785970--2786137 Score: 225
Period size: 61 Copynumber: 2.8 Consensus size: 61
2785960 AGGCCAGTGA
* * *
2785970 TGTCGATATGCTGATTCAAGGCCAGC-A-ATGTCGAAGTTGAAGATGAGAAGAATGATAATGG
1 TGTCGATATGCTGATTCAAGGCCAGCGATAT-TGGAA-TTGAAGATGAGAAAAATGATAAAGG
*
2786031 T-TCCGATATGCTGATTCAAGGCCAACGATATTGGAATTGAAGATGAGAAAAATGATAAAGG
1 TGT-CGATATGCTGATTCAAGGCCAGCGATATTGGAATTGAAGATGAGAAAAATGATAAAGG
* * *
2786092 TGTCGATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGATGA
1 TGTCGATATGCTGATTCAAGGCCAGCGATATTGGAATTGAAGATGA
2786138 TAAGGGTGAG
Statistics
Matches: 95, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
60 1 0.01
61 86 0.91
62 6 0.06
63 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (61 bp):
TGTCGATATGCTGATTCAAGGCCAGCGATATTGGAATTGAAGATGAGAAAAATGATAAAGG
Found at i:2786394 original size:52 final size:52
Alignment explanation
Indices: 2786152--2786405 Score: 203
Period size: 52 Copynumber: 4.9 Consensus size: 52
2786142 GGTGAGAAGA
* * * * ** *
2786152 GTGCCAACGTGCTGATTCACGGCTAGCGACATTAGACTTGAAGACGGGAAGAA-
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTAGACTT-AAGA-AAGAAAAAG
* ** * * * *
2786205 -TGCCAATGTGCTGATTCAAGGCTAGTGACA-TCGATCTTAGGAATGATAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTAGA-CTTAAGAAAGAAAAAG
* * * * * * *
2786256 ATGCCAATATGCTGATTCAAGGCCAGCAATATCAAACTT-AGAGATGACAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTAGACTTAAGA-AAGAAAAAG
* * * *
2786308 GTGCCAATATACTGATTCAAGGCCAGCAATATTGGACTTAAGAAAGAAAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTAGACTTAAGAAAGAAAAAG
*
2786360 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAA-AAAGA
1 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTAGACTTAAGAAAGA
2786406 GATGGTTTGA
Statistics
Matches: 166, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
50 4 0.02
51 13 0.08
52 145 0.87
53 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (52 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCAACATTAGACTTAAGAAAGAAAAAG
Found at i:2786512 original size:33 final size:34
Alignment explanation
Indices: 2786475--2786589 Score: 112
Period size: 33 Copynumber: 3.4 Consensus size: 34
2786465 GATGCCACCG
2786475 ACTTGTGTGGGCTTTTAAAG-GAGGCTGCCA-CTA
1 ACTTGTGTGGGCTTTTAAAGAGAGGCTGCCATC-A
* * *
2786508 ACTTGTGTGGGC-TTTAAAGAGGGGTTGCCATCG
1 ACTTGTGTGGGCTTTTAAAGAGAGGCTGCCATCA
* * * *
2786541 ACTTGTGTGGGC-TTTAGAGAAGGGGTTGCCATCG
1 ACTTGTGTGGGCTTTTAAAG-AGAGGCTGCCATCA
*
2786575 GCTTGTGTGGGCTTT
1 ACTTGTGTGGGCTTT
2786590 AGAGAATGGT
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
32 7 0.10
33 38 0.52
34 26 0.36
35 2 0.03
ACGTcount: A:0.17, C:0.16, G:0.36, T:0.32
Consensus pattern (34 bp):
ACTTGTGTGGGCTTTTAAAGAGAGGCTGCCATCA
Found at i:2786643 original size:32 final size:32
Alignment explanation
Indices: 2786451--2786755 Score: 278
Period size: 32 Copynumber: 9.4 Consensus size: 32
2786441 CCAATGACAT
*
2786451 TGGGC-TT-AGAAGGAGATGCCACCGACTTGTG
1 TGGGCTTTGAGAAGG-GTTGCCACCGACTTGTG
* * **
2786482 TGGGCTTTTA-AAGGAGGCTGCCACTAACTTGTG
1 TGGGCTTTGAGAA-G-GGTTGCCACCGACTTGTG
* * *
2786515 TGGGCTTTAAAGAGGGGTTGCCATCGACTTGTG
1 TGGGCTTT-GAGAAGGGTTGCCACCGACTTGTG
* *
2786548 TGGGCTTTAGAGAAGGGGTTGCCATCGGCTTGTG
1 TGGGCTTT-GAGAA-GGGTTGCCACCGACTTGTG
* ** *
2786582 TGGGCTTTAGAGAATGGTTGCCATTGACTTATG
1 TGGGCTTT-GAGAAGGGTTGCCACCGACTTGTG
* * *
2786615 TAGGCTTTTAGAAGGGTTGCCACCGACTTATG
1 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTG
* ** *
2786647 TGGGCTTTAAGAAGGGTTGCCATTGGCTTGTG
1 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTG
* *
2786679 TGGGCTTTGAGAAAGGTTGCCA-CGACTTCTG
1 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTG
* *
2786710 TAGGG-TTTAAGAAGGGTTGCCACCGGCTTGTG
1 T-GGGCTTTGAGAAGGGTTGCCACCGACTTGTG
2786742 TGGGCTTTGAGAAG
1 TGGGCTTTGAGAAG
2786756 TATACGCTTT
Statistics
Matches: 227, Mismatches: 37, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
31 30 0.13
32 89 0.39
33 72 0.32
34 35 0.15
35 1 0.00
ACGTcount: A:0.19, C:0.16, G:0.35, T:0.30
Consensus pattern (32 bp):
TGGGCTTTGAGAAGGGTTGCCACCGACTTGTG
Found at i:2786738 original size:63 final size:65
Alignment explanation
Indices: 2786451--2786988 Score: 373
Period size: 64 Copynumber: 8.2 Consensus size: 65
2786441 CCAATGACAT
* * * * **
2786451 TGGGC-TT-AGAAGGAGATGCCACCGACTTGTGTGGGCTTTTA-AAGGAGGCTGCCACTAACTTG
1 TGGGCTTTAAGAAGG-GTTGCCATCGACTTGTGTGGGCTTTGAGAA-GAGGTTGCCACCGACTTG
2786513 TG
64 TG
* * * *
2786515 TGGGCTTTAAAGAGGGGTTGCCATCGACTTGTGTGGGCTTTAGAGAAGGGGTTGCCATCGGCTTG
1 TGGGCTTT-AAGAAGGGTTGCCATCGACTTGTGTGGGCTTT-GAGAAGAGGTTGCCACCGACTTG
2786580 TG
64 TG
* * * * * *
2786582 TGGGCTTTAGAGAATGGTTGCCATTGACTTATGTAGGCTTTTAGAAG-GGTTGCCACCGACTTAT
1 TGGGCTTTA-AGAAGGGTTGCCATCGACTTGTGTGGGCTTTGAGAAGAGGTTGCCACCGACTTGT
2786646 G
65 G
* * *
2786647 TGGGCTTTAAGAAGGGTTGCCATTGGCTTGTGTGGGCTTTGAGAA-AGGTTGCCA-CGACTTCTG
1 TGGGCTTTAAGAAGGGTTGCCATCGACTTGTGTGGGCTTTGAGAAGAGGTTGCCACCGACTTGTG
* * * **
2786710 TAGGG-TTTAAGAAGGGTTGCCACCGGCTTGTGTGGGCTTTGAGAAGTATACGCTTTGAGAAGGG
1 T-GGGCTTTAAGAAGGGTTGCCATCGACTTGTGTGGGCTTTGAGAAG---A-G-GTTG-CCA---
* *
2786774 TTGCCAACTTGTA
56 ---CCGACTTGTG
* * * * * *
2786787 TAGGCTTTGAGAAGAGTTGCCA-CCAGCTTGTGTGGGCTTTGAGAA-AGGTTGCCACTGGCTTGT
1 TGGGCTTTAAGAAGGGTTGCCATCGA-CTTGTGTGGGCTTTGAGAAGAGGTTGCCACCGACTTGT
2786850 G
65 G
* * * * * * * * *
2786851 TGGACTTTGAGAAGGGTTGCCACCGGCTTGTGTGGGCTTTGATAAG-GGTTGCTACCGAGTTCTA
1 TGGGCTTTAAGAAGGGTTGCCATCGACTTGTGTGGGCTTTGAGAAGAGGTTGCCACCGACTTGTG
* * * * * *
2786915 AGGGCTTTGAGAAGGGTTGCCATTGACTTGTGTAGGCTTTAAG-AG-GGTTGCCA-CTAGCTTGT
1 TGGGCTTTAAGAAGGGTTGCCATCGACTTGTGTGGGCTTTGAGAAGAGGTTGCCACCGA-CTTGT
2786977 G
65 G
*
2786978 TTGGCTTTAAG
1 TGGGCTTTAAG
2786989 GAAAAAAGTG
Statistics
Matches: 374, Mismatches: 73, Indels: 55
0.75 0.15 0.11
Matches are distributed among these distances:
62 2 0.01
63 67 0.18
64 137 0.37
65 27 0.07
66 29 0.08
67 55 0.15
68 3 0.01
69 3 0.01
70 2 0.01
71 3 0.01
72 1 0.00
73 1 0.00
76 3 0.01
77 41 0.11
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.31
Consensus pattern (65 bp):
TGGGCTTTAAGAAGGGTTGCCATCGACTTGTGTGGGCTTTGAGAAGAGGTTGCCACCGACTTGTG
Found at i:2786816 original size:77 final size:78
Alignment explanation
Indices: 2786682--2786831 Score: 221
Period size: 77 Copynumber: 1.9 Consensus size: 78
2786672 GCTTGTGTGG
* * * *
2786682 GCTTTGAGAAAGGTTGCCACGACTTCTGTAGGGTTTAAGAAGGGTTGCCACCGGCTTGTGTGGGC
1 GCTTTGAGAAAGGTTGCCAC-ACTTCTATAGGCTTTAAGAAGAGTTGCCACCAGCTTGTGTGGGC
2786747 TTTGAGAAGTATAC
65 TTTGAGAAGTATAC
* * *
2786761 GCTTTGAGAAGGGTTGCCA-ACTTGTATAGGCTTTGAGAAGAGTTGCCACCAGCTTGTGTGGGCT
1 GCTTTGAGAAAGGTTGCCACACTTCTATAGGCTTTAAGAAGAGTTGCCACCAGCTTGTGTGGGCT
2786825 TTGAGAA
66 TTGAGAA
2786832 AGGTTGCCAC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
77 46 0.72
79 18 0.28
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (78 bp):
GCTTTGAGAAAGGTTGCCACACTTCTATAGGCTTTAAGAAGAGTTGCCACCAGCTTGTGTGGGCT
TTGAGAAGTATAC
Found at i:2786825 original size:32 final size:32
Alignment explanation
Indices: 2786761--2786985 Score: 219
Period size: 32 Copynumber: 7.2 Consensus size: 32
2786751 AGAAGTATAC
* *
2786761 GCTTTGAGAAGGGTTGCCA--A-CTTGTATAG
1 GCTTTGAGAAGGGTTGCCACCAGCTTGTGTGG
*
2786790 GCTTTGAGAAGAGTTGCCACCAGCTTGTGTGG
1 GCTTTGAGAAGGGTTGCCACCAGCTTGTGTGG
* **
2786822 GCTTTGAGAAAGGTTGCCACTGGCTTGTGTGG
1 GCTTTGAGAAGGGTTGCCACCAGCTTGTGTGG
* *
2786854 ACTTTGAGAAGGGTTGCCACCGGCTTGTGTGG
1 GCTTTGAGAAGGGTTGCCACCAGCTTGTGTGG
* * * **
2786886 GCTTTGATAAGGGTTGCTACCGAG-TTCTAAGG
1 GCTTTGAGAAGGGTTGCCACC-AGCTTGTGTGG
** *
2786918 GCTTTGAGAAGGGTTGCCA-TTGACTTGTGTAG
1 GCTTTGAGAAGGGTTGCCACCAG-CTTGTGTGG
* * *
2786950 GCTTTAAG-AGGGTTGCCACTAGCTTGTGTTG
1 GCTTTGAGAAGGGTTGCCACCAGCTTGTGTGG
2786981 GCTTT
1 GCTTT
2786986 AAGGAAAAAA
Statistics
Matches: 161, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
29 18 0.11
30 1 0.01
31 24 0.15
32 117 0.73
33 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (32 bp):
GCTTTGAGAAGGGTTGCCACCAGCTTGTGTGG
Found at i:2787157 original size:30 final size:30
Alignment explanation
Indices: 2787123--2787331 Score: 104
Period size: 30 Copynumber: 6.8 Consensus size: 30
2787113 GAAAAAAAAA
2787123 AGATGCCACTAAGTCGTGGACTTGAAGAAG
1 AGATGCCACTAAGTCGTGGACTTGAAGAAG
* ** * *
2787153 AGATGCTACTAAGTCGTTAACTTTAGGAA-
1 AGATGCCACTAAGTCGTGGACTTGAAGAAG
* * * *
2787182 AG-GGACCACGAAGTCGTGGGCTTTTGGTTA-AAG
1 AGATG-CCACTAAGTCGTGGAC--TT-G-AAGAAG
* * * *
2787215 -GGTGCCAC-AGAGTTGTGGGCTTTGAAAAGAAAA
1 AGATGCCACTA-AGTCGTGGAC-TTG--AAG-AAG
* * *
2787248 AGGATGCCACTGAGTTGTGGACTTGGAGAAG
1 A-GATGCCACTAAGTCGTGGACTTGAAGAAG
* * *
2787279 AGATGCCACTGAGTTGTGGACTTGGAGAAG
1 AGATGCCACTAAGTCGTGGACTTGAAGAAG
*
2787309 AGATGCCACTAAGTCATGGACTT
1 AGATGCCACTAAGTCGTGGACTT
2787332 TAGGAAGGGT
Statistics
Matches: 138, Mismatches: 27, Indels: 28
0.72 0.14 0.15
Matches are distributed among these distances:
28 1 0.01
29 13 0.09
30 74 0.54
31 10 0.07
32 18 0.13
33 3 0.02
34 3 0.02
35 16 0.12
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.24
Consensus pattern (30 bp):
AGATGCCACTAAGTCGTGGACTTGAAGAAG
Found at i:2792264 original size:52 final size:52
Alignment explanation
Indices: 2792183--2792303 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
2792173 TGAAAAGTTA
*
2792183 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
2792235 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
2792287 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
2792304 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:2792316 original size:52 final size:51
Alignment explanation
Indices: 2792183--2792323 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
2792173 TGAAAAGTTA
2792183 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
2792235 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
2792287 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2792324 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:2792330 original size:13 final size:13
Alignment explanation
Indices: 2792312--2792336 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2792302 CAAAGATCAG
2792312 TGTATCGATACAA
1 TGTATCGATACAA
2792325 TGTATCGATACA
1 TGTATCGATACA
2792337 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2792418 original size:33 final size:33
Alignment explanation
Indices: 2792376--2792445 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2792366 GGCAGTAGCT
2792376 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
2792409 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
2792442 TACA
1 TACA
2792446 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:2792419 original size:13 final size:13
Alignment explanation
Indices: 2792401--2792425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2792391 CAAAAAAATA
2792401 TGTATCGATACAT
1 TGTATCGATACAT
2792414 TGTATCGATACA
1 TGTATCGATACA
2792426 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2807902 original size:58 final size:56
Alignment explanation
Indices: 2807765--2807908 Score: 188
Period size: 52 Copynumber: 2.6 Consensus size: 56
2807755 CATATTTGGT
* *
2807765 GCTATTCATCATCCATAAAAAAAAGAAAAAAAAAAGTGTCCTAGAATTTTAACCTTTG
1 GCTATTCATCATCCA-AAAAAAAA-AAAAAAAGAAGTGTCCTAGAATTCTAACCTTTG
* *
2807823 GCTATTCATCATCC----TAAAAAAAAAAAGAAGTGTTCTAGAATTCTAACCTTTG
1 GCTATTCATCATCCAAAAAAAAAAAAAAAAGAAGTGTCCTAGAATTCTAACCTTTG
2807875 GCTATTCATCATCCCAAAAAAGAAAAAAAAAAGA
1 GCTATTCATCAT-CCAAAAAA-AAAAAAAAAAGA
2807909 TAGTTGTTAG
Statistics
Matches: 75, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
52 42 0.56
53 6 0.08
57 1 0.01
58 26 0.35
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (56 bp):
GCTATTCATCATCCAAAAAAAAAAAAAAAAGAAGTGTCCTAGAATTCTAACCTTTG
Found at i:2807997 original size:28 final size:28
Alignment explanation
Indices: 2807963--2808034 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
2807953 TTCTTCTTTG
* *
2807963 TTGATTTCTTTTCCTTTGAAATTTCTTA
1 TTGATTTCATTTCCTTTCAAATTTCTTA
* *
2807991 TTTATTTCATTTCCTTTCATATTTCTTA
1 TTGATTTCATTTCCTTTCAAATTTCTTA
*
2808019 TTGATTTCACTTCCTT
1 TTGATTTCATTTCCTT
2808035 AATCTTTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.17, C:0.18, G:0.04, T:0.61
Consensus pattern (28 bp):
TTGATTTCATTTCCTTTCAAATTTCTTA
Found at i:2816203 original size:19 final size:18
Alignment explanation
Indices: 2816179--2816241 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
2816169 TATCATACAA
2816179 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
2816198 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
*
2816211 TGTATCAATACATAAGTTT
1 TGTATCGATACATAAG-TT
2816230 TGTATCGATACA
1 TGTATCGATACA
2816242 ATGTATCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:2816211 original size:32 final size:32
Alignment explanation
Indices: 2816166--2816249 Score: 143
Period size: 32 Copynumber: 2.7 Consensus size: 32
2816156 TTTCAACAAT
*
2816166 TTGTATC-ATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCAATACATAAGTG
*
2816197 TTGTATCGATACAATGTATCAATACATAAGTT
1 TTGTATCGATACAATGTATCAATACATAAGTG
2816229 TTGTATCGATACAATGTATCA
1 TTGTATCGATACAATGTATCA
2816250 CTACGAAGCT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 7 0.14
32 43 0.86
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCAATACATAAGTG
Found at i:2816320 original size:34 final size:34
Alignment explanation
Indices: 2816273--2816354 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
2816263 GCAAAGGAAA
*
2816273 TGTATCGATACATTACTCAAATGTATTGATACAT
1 TGTATCGATACATTACTCAAATGTATCGATACAT
* *
2816307 TGTCTCGATACATTACTTAAATGTATCGATACAT
1 TGTATCGATACATTACTCAAATGTATCGATACAT
2816341 TGTATCGATACATT
1 TGTATCGATACATT
2816355 GATCTTTGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (34 bp):
TGTATCGATACATTACTCAAATGTATCGATACAT
Found at i:2816346 original size:13 final size:13
Alignment explanation
Indices: 2816328--2816355 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2816318 ATTACTTAAA
2816328 TGTATCGATACAT
1 TGTATCGATACAT
2816341 TGTATCGATACAT
1 TGTATCGATACAT
2816354 TG
1 TG
2816356 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2820105 original size:19 final size:17
Alignment explanation
Indices: 2820081--2820136 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
2820071 TTCAAACTCC
2820081 ATATTTATCTCAATAAAT
1 ATATTTATCT-AATAAAT
2820099 AATATTTATCTAATAAAT
1 -ATATTTATCTAATAAAT
* *
2820117 ATAATTATCTAATAATT
1 ATATTTATCTAATAAAT
2820134 ATA
1 ATA
2820137 AAATTAGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 18 0.51
18 7 0.20
19 10 0.29
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTTATCTAATAAAT
Found at i:2826298 original size:21 final size:21
Alignment explanation
Indices: 2826260--2826299 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2826250 GAGTAGTTAA
*
2826260 TACAATAACTCTATTATTCAT
1 TACAATAACTATATTATTCAT
2826281 TACAA-AACTATATCTATTC
1 TACAATAACTATAT-TATTC
2826300 TTATACCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (21 bp):
TACAATAACTATATTATTCAT
Found at i:2830165 original size:12 final size:12
Alignment explanation
Indices: 2830145--2830179 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
2830135 AAGAGAAAGA
2830145 AGAGATAGGAGG
1 AGAGATAGGAGG
2830157 -GATGATAGGAGG
1 AGA-GATAGGAGG
2830169 AGAGATAGGAG
1 AGAGATAGGAG
2830180 AGATAGGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (12 bp):
AGAGATAGGAGG
Found at i:2830180 original size:9 final size:9
Alignment explanation
Indices: 2830166--2830203 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
2830156 GGATGATAGG
2830166 AGGAGAGAT
1 AGGAGAGAT
2830175 AGGAGAGAT
1 AGGAGAGAT
2830184 AGGAGAGAT
1 AGGAGAGAT
*
2830193 AGTAGAGAT
1 AGGAGAGAT
2830202 AG
1 AG
2830204 AAGGGATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:2830200 original size:51 final size:51
Alignment explanation
Indices: 2830136--2830235 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 51
2830126 TAGCCCTCAA
* * *
2830136 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAGG
1 AGAGAAAGAAGAGATAGAAGGGATGATACGAGGAAAGATAGGAGAGATAGG
* *
2830187 AGAGATAGTAGAGATAGAAGGGATGATACGAGGAAAGATAGGAGAGATA
1 AGAGAAAGAAGAGATAGAAGGGATGATACGAGGAAAGATAGGAGAGATA
2830236 ATAGAGAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.46, C:0.01, G:0.41, T:0.12
Consensus pattern (51 bp):
AGAGAAAGAAGAGATAGAAGGGATGATACGAGGAAAGATAGGAGAGATAGG
Found at i:2830226 original size:42 final size:42
Alignment explanation
Indices: 2830175--2830254 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
2830165 GAGGAGAGAT
* * *
2830175 AGGAGAGATAGGAGAGATAGTAGAGATAGAAGGGATGATACG
1 AGGAAAGATAGGAGAGATAATAGAGAGAGAAGGGATGATACG
*
2830217 AGGAAAGATAGGAGAGATAATAGAGAGAGGAGGGATGA
1 AGGAAAGATAGGAGAGATAATAGAGAGAGAAGGGATGA
2830255 CAGGAGGAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.45, C:0.01, G:0.41, T:0.12
Consensus pattern (42 bp):
AGGAAAGATAGGAGAGATAATAGAGAGAGAAGGGATGATACG
Found at i:2832340 original size:20 final size:20
Alignment explanation
Indices: 2832317--2832389 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2832307 ACAATTCAAA
2832317 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2832337 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
2832358 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2832378 GTATCGATACAT
1 GTATCGATACAT
2832390 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2832360 original size:21 final size:21
Alignment explanation
Indices: 2832334--2832410 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
2832324 TACATGTTGC
2832334 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
2832355 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
2832375 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
2832395 AGATGTATCGATACAT
1 A-ATGTATCGATACAT
2832411 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:2832368 original size:41 final size:41
Alignment explanation
Indices: 2832317--2832410 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
2832307 ACAATTCAAA
2832317 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAA-AT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAAGAT
2832358 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2832399 GTATCGATACAT
1 GTATCGATACAT
2832411 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 6 0.12
41 46 0.88
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2832467 original size:13 final size:13
Alignment explanation
Indices: 2832449--2832474 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2832439 TACAGCAAGT
2832449 ATGTATCGATACA
1 ATGTATCGATACA
2832462 ATGTATCGATACA
1 ATGTATCGATACA
2832475 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2836552 original size:15 final size:15
Alignment explanation
Indices: 2836532--2836562 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2836522 TAAAAATGTC
*
2836532 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2836547 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2836562 C
1 C
2836563 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2838651 original size:13 final size:13
Alignment explanation
Indices: 2838633--2838671 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2838623 ACATTTTTCC
2838633 TTGTATCGATACA
1 TTGTATCGATACA
2838646 TTGTATCGATACA
1 TTGTATCGATACA
*
2838659 CTGTATCGATACA
1 TTGTATCGATACA
2838672 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2840530 original size:33 final size:33
Alignment explanation
Indices: 2840464--2840558 Score: 183
Period size: 33 Copynumber: 2.9 Consensus size: 33
2840454 AATTTTGATA
2840464 TGAATTACTTGATTAAGGGGGAGA-TTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTTTT
2840496 TGAATTACTTGATTAAGGGGGAGATTTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTTTT
2840529 TGAATTACTTGATTAAGGGGGAGATTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTT
2840559 AATAAACGGG
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 24 0.39
33 38 0.61
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.46
Consensus pattern (33 bp):
TGAATTACTTGATTAAGGGGGAGATTTTTTTTT
Found at i:2841202 original size:20 final size:20
Alignment explanation
Indices: 2841179--2841251 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2841169 ACAATTCAAA
2841179 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2841199 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
2841220 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2841240 GTATCGATACAT
1 GTATCGATACAT
2841252 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2841222 original size:21 final size:21
Alignment explanation
Indices: 2841196--2841272 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
2841186 TACATGTTGC
2841196 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
2841217 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
2841237 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
2841257 AGATGTATCGATACAT
1 A-ATGTATCGATACAT
2841273 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:2841230 original size:41 final size:41
Alignment explanation
Indices: 2841179--2841272 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
2841169 ACAATTCAAA
2841179 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAA-AT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAAGAT
2841220 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2841261 GTATCGATACAT
1 GTATCGATACAT
2841273 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 6 0.12
41 46 0.88
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2841329 original size:13 final size:13
Alignment explanation
Indices: 2841311--2841336 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2841301 TACAGCAAGT
2841311 ATGTATCGATACA
1 ATGTATCGATACA
2841324 ATGTATCGATACA
1 ATGTATCGATACA
2841337 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2844084 original size:33 final size:34
Alignment explanation
Indices: 2844038--2844128 Score: 114
Period size: 33 Copynumber: 2.7 Consensus size: 34
2844028 TTCTTCTCTC
* *
2844038 CTCCTCCTGTCATCCCTCCTCTCTCCAT-TATCT
1 CTCCTCCTATCATCCCTCCTATCTCCATCTATCT
* *
2844071 CTCCTTCTATCATCCCTCCTATCT-CTTCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCCATCTATCT
* *
2844104 CGCCTCCTATCATACCTCCTATCTC
1 CTCCTCCTATCATCCCTCCTATCTC
2844129 TTTTTTCTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.04
33 47 0.96
ACGTcount: A:0.12, C:0.46, G:0.02, T:0.40
Consensus pattern (34 bp):
CTCCTCCTATCATCCCTCCTATCTCCATCTATCT
Found at i:2844092 original size:12 final size:11
Alignment explanation
Indices: 2844040--2844128 Score: 51
Period size: 12 Copynumber: 8.0 Consensus size: 11
2844030 CTTCTCTCCT
*
2844040 CCTCCTGTCATC
1 CCTCCTATC-TC
*
2844052 CCTCCTCTCTC
1 CCTCCTATCTC
*
2844063 CAT--TATCTC
1 CCTCCTATCTC
*
2844072 TCCTTCTATCATC
1 -CCTCCTATC-TC
2844085 CCTCCTATCT-
1 CCTCCTATCTC
*
2844095 -CTTCTATCTC
1 CCTCCTATCTC
*
2844105 GCCTCCTATCATA
1 -CCTCCTATC-TC
2844118 CCTCCTATCTC
1 CCTCCTATCTC
2844129 TTTTTTCTCT
Statistics
Matches: 60, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
9 13 0.22
10 2 0.03
11 6 0.10
12 36 0.60
13 3 0.05
ACGTcount: A:0.12, C:0.46, G:0.02, T:0.39
Consensus pattern (11 bp):
CCTCCTATCTC
Found at i:2844100 original size:21 final size:21
Alignment explanation
Indices: 2844074--2844114 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2844064 ATTATCTCTC
2844074 CTTCTATCATC-CCTCCTATCT
1 CTTCTATC-TCGCCTCCTATCT
2844095 CTTCTATCTCGCCTCCTATC
1 CTTCTATCTCGCCTCCTATC
2844115 ATACCTCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.12, C:0.44, G:0.02, T:0.41
Consensus pattern (21 bp):
CTTCTATCTCGCCTCCTATCT
Found at i:2853501 original size:9 final size:9
Alignment explanation
Indices: 2853489--2853591 Score: 78
Period size: 9 Copynumber: 12.1 Consensus size: 9
2853479 CTCTCTCTAT
2853489 TATCTCTCC
1 TATCTCTCC
2853498 TATCTCTCC
1 TATCTCTCC
* *
2853507 T-CCTAT-C
1 TATCTCTCC
*
2853514 -ATCCCTCC
1 TATCTCTCC
2853522 TATCTC-CAC
1 TATCTCTC-C
2853531 TATCTCTCC
1 TATCTCTCC
2853540 TATCTCTCC
1 TATCTCTCC
* *
2853549 T-CCTAT-C
1 TATCTCTCC
*
2853556 -ATCCCTCC
1 TATCTCTCC
2853564 TATCTC-CAC
1 TATCTCTC-C
2853573 TATCTCTCC
1 TATCTCTCC
2853582 TATCTCTCC
1 TATCTCTCC
2853591 T
1 T
2853592 CCTATCATCC
Statistics
Matches: 72, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
7 6 0.08
8 10 0.14
9 54 0.75
10 2 0.03
ACGTcount: A:0.14, C:0.47, G:0.00, T:0.40
Consensus pattern (9 bp):
TATCTCTCC
Found at i:2853509 original size:12 final size:12
Alignment explanation
Indices: 2853494--2853612 Score: 88
Period size: 12 Copynumber: 10.9 Consensus size: 12
2853484 TCTATTATCT
2853494 CTCCTATCTCTC
1 CTCCTATCTCTC
2853506 CTCCTATCATC-C
1 CTCCTATC-TCTC
2853518 CTCCTA--TCTC
1 CTCCTATCTCTC
*
2853528 C-ACTA--TCT-
1 CTCCTATCTCTC
2853536 CTCCTATCTCTC
1 CTCCTATCTCTC
2853548 CTCCTATCATC-C
1 CTCCTATC-TCTC
2853560 CTCCTA--TCTC
1 CTCCTATCTCTC
*
2853570 C-ACTA--TCT-
1 CTCCTATCTCTC
2853578 CTCCTATCTCTC
1 CTCCTATCTCTC
2853590 CTCCTATCATC-C
1 CTCCTATC-TCTC
2853602 CTCCTATCTCT
1 CTCCTATCTCT
2853613 TCTTTCTCTT
Statistics
Matches: 89, Mismatches: 4, Indels: 28
0.74 0.03 0.23
Matches are distributed among these distances:
8 2 0.02
9 22 0.25
10 4 0.04
11 8 0.09
12 47 0.53
13 6 0.07
ACGTcount: A:0.13, C:0.48, G:0.00, T:0.39
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:2853567 original size:33 final size:30
Alignment explanation
Indices: 2853506--2853582 Score: 86
Period size: 33 Copynumber: 2.5 Consensus size: 30
2853496 CCTATCTCTC
2853506 CTCCTATCATC-CCTCCTATCTCCACTATCT
1 CTCCTATC-TCTCCTCCTATCTCCACTATCT
*
2853536 CTCCTATCTCTCCTCCTATCATCCCTCCTATCT
1 CTCCTATCTCTCCTCCTATC-T-CC-ACTATCT
2853569 C-CACTATCTCTCCT
1 CTC-CTATCTCTCCT
2853583 ATCTCTCCTC
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
29 2 0.05
30 17 0.41
31 1 0.02
32 3 0.07
33 18 0.44
ACGTcount: A:0.14, C:0.48, G:0.00, T:0.38
Consensus pattern (30 bp):
CTCCTATCTCTCCTCCTATCTCCACTATCT
Found at i:2853621 original size:42 final size:42
Alignment explanation
Indices: 2853461--2853611 Score: 266
Period size: 42 Copynumber: 3.6 Consensus size: 42
2853451 TTCTTCTCTC
* * * *
2853461 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCCACTATCTCTCCTATCT
2853503 CTCCTCCTATCATCCCTCCTATCTCCACTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCCACTATCTCTCCTATCT
2853545 CTCCTCCTATCATCCCTCCTATCTCCACTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCCACTATCTCTCCTATCT
2853587 CTCCTCCTATCATCCCTCCTATCTC
1 CTCCTCCTATCATCCCTCCTATCTC
2853612 TTCTTTCTCT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 105 1.00
ACGTcount: A:0.13, C:0.48, G:0.01, T:0.39
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCCACTATCTCTCCTATCT
Found at i:2859030 original size:19 final size:22
Alignment explanation
Indices: 2858987--2859032 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2858977 AAGATGAAAG
*
2858987 AAAAGAAAATGAGTGTATGAGA
1 AAAAGAAAATCAGTGTATGAGA
2859009 AAAAGAAAA-CAGTG-AT-AGA
1 AAAAGAAAATCAGTGTATGAGA
2859028 AAAAG
1 AAAAG
2859033 TAAGTGTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 2 0.09
21 4 0.17
22 9 0.39
ACGTcount: A:0.61, C:0.02, G:0.24, T:0.13
Consensus pattern (22 bp):
AAAAGAAAATCAGTGTATGAGA
Found at i:2862006 original size:139 final size:136
Alignment explanation
Indices: 2861695--2862176 Score: 557
Period size: 139 Copynumber: 3.5 Consensus size: 136
2861685 GTTTGCATTA
* * * * *
2861695 GTGGGCTTTTTGGGTGC-CGCAAGCTCATACAAGCTTTGAGAAAAGATGTCACCAGCTCATGTGG
1 GTGGGCTTTTTGGGTGCTCGCAAGCTCATGCAAGCTTTAAGAAAGGATGCCACCAGCTCGTGTGG
* * *
2861759 GCTTTTAGGAAGGTTCGAGTGCC-CCAGCTTGTG-TGG-GTTTTGGAAAGGTTTAAGTGCCACTA
66 GCTTTTAGGAAGGTTCGAGTGCCACCAGCTTGTGTTGGCATTTTGGAAAGGTTTTAGTGCCACCA
2861821 ACTTGT
131 ACTTGT
*
2861827 GTAGGCAGGCTTTTTGGGTGCT-GCAAGCTCATGCAAGCTTTAAGAAAGGATGCCACTAGCTCGT
1 GT--G--GGCTTTTTGGGTGCTCGCAAGCTCATGCAAGCTTTAAGAAAGGATGCCACCAGCTCGT
* * * *
2861891 GTGGGCTTTTGGGAAGGCTCGAGTGCCACCAGCTTGTGTTGGCTTTTTGAAAAGGTTTTCA-TGC
62 GTGGGCTTTTAGGAAGGTTCGAGTGCCACCAGCTTGTGTTGGCATTTTGGAAAGGTTTT-AGTGC
*
2861955 CACCAACTTAT
126 CACCAACTTGT
* * * *
2861966 GTGGGTTTTTTGGGTGCTGCCCGCCAGCTCATGCAGGCTTTAAGAAAGGATGTCACCAGCTCGTG
1 GTGGGCTTTTTGGGTGCT---CGCAAGCTCATGCAAGCTTTAAGAAAGGATGCCACCAGCTCGTG
* * * *
2862031 TGGGATTTTAGGAAGGTTCGAGTGCCACAAACTTGTGTGGGCATTTTGGAAAGGTTTTAGTGCCA
63 TGGGCTTTTAGGAAGGTTCGAGTGCCACCAGCTTGTGTTGGCATTTTGGAAAGGTTTTAGTGCCA
2862096 CCAACTTGT
128 CCAACTTGT
* * ** *
2862105 GTGGGCTTTTTGAGTG-TCACCAA-CTCATGCGGGCTTTTTGAGAAAGGATGCCACCAGCTCGTG
1 GTGGGCTTTTTGGGTGCTC-GCAAGCTCATGCAAGC--TTTAAGAAAGGATGCCACCAGCTCGTG
*
2862168 TGGGTTTTT
63 TGGGCTTTT
2862177 TGGGTTACTC
Statistics
Matches: 298, Mismatches: 35, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
132 2 0.01
134 1 0.00
135 25 0.08
136 77 0.26
137 44 0.15
138 5 0.02
139 143 0.48
140 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (136 bp):
GTGGGCTTTTTGGGTGCTCGCAAGCTCATGCAAGCTTTAAGAAAGGATGCCACCAGCTCGTGTGG
GCTTTTAGGAAGGTTCGAGTGCCACCAGCTTGTGTTGGCATTTTGGAAAGGTTTTAGTGCCACCA
ACTTGT
Found at i:2862085 original size:38 final size:37
Alignment explanation
Indices: 2862028--2862116 Score: 117
Period size: 38 Copynumber: 2.4 Consensus size: 37
2862018 TCACCAGCTC
2862028 GTGTGGG-ATTTTAGGAAGGTTCGAGTGCCACAAACTT
1 GTGTGGGCATTTT-GGAAGGTTCGAGTGCCACAAACTT
** *
2862065 GTGTGGGCATTTTGGAAAGGTTTTAGTGCCACCAACTT
1 GTGTGGGCATTTTGG-AAGGTTCGAGTGCCACAAACTT
*
2862103 GTGTGGGCTTTTTG
1 GTGTGGGCATTTTG
2862117 AGTGTCACCA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
37 9 0.20
38 37 0.80
ACGTcount: A:0.19, C:0.13, G:0.33, T:0.35
Consensus pattern (37 bp):
GTGTGGGCATTTTGGAAGGTTCGAGTGCCACAAACTT
Found at i:2862125 original size:28 final size:28
Alignment explanation
Indices: 2862085--2862146 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
2862075 TTTGGAAAGG
** *
2862085 TTTT-AGTGCCACCAACTTGTGTGGGCT
1 TTTTGAGTGCCACCAACTCATGCGGGCT
*
2862112 TTTTGAGTGTCACCAACTCATGCGGGCT
1 TTTTGAGTGCCACCAACTCATGCGGGCT
2862140 TTTTGAG
1 TTTTGAG
2862147 AAAGGATGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 4 0.13
28 26 0.87
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (28 bp):
TTTTGAGTGCCACCAACTCATGCGGGCT
Found at i:2862553 original size:143 final size:144
Alignment explanation
Indices: 2862225--2862582 Score: 474
Period size: 143 Copynumber: 2.5 Consensus size: 144
2862215 TAAATGATTG
* * **
2862225 TGATAGGTGTCTAATTCTAACAAATTTGGTGCCACCAATATTGGCAGGCTTTGAAAAAAGATTGG
1 TGATAGGTGTCTGATTCTAACAAATTTGGTGCCACCAGTATTGGTGGGCTTTGAAAAAAGATTGG
* *
2862290 GTGCCACCAGCTCATGTGGGCTTTTTAGAGAAAAGATTTGGAAGATTAAGATTTACTTCACAGGG
66 GTGCCACCAGCTCATGTGGGCTTTTTAGAGAAAAGATTTAGAAGATTAAGATTTACTCCACAGGG
2862355 GATTGACACAACTA
131 GATTGACACAACTA
** *
2862369 TGACT-GGTGTCTGACTT-TAACAAATTTGGTGCCACTTGTATTGGTGGGCTTTGAAAAGAGATT
1 TGA-TAGGTGTCTGA-TTCTAACAAATTTGGTGCCACCAGTATTGGTGGGCTTTGAAAAAAGATT
* * * *
2862432 GGGTGCTAGCAGCTCATGTGGGC-TTTTGGAGAAAAGATTTAGAGGATTAAGATTTACTCCACTA
64 GGGTGCCACCAGCTCATGTGGGCTTTTTAGAGAAAAGATTTAGAAGATTAAGATTTACTCCAC-A
* *
2862496 -GGGATTGACACAATTC
128 GGGGATTGACACAACTA
* * * * *
2862512 TGATAAGTGTCTGGTTCTAACAAATTCGGTGCCTCCAGTATTGGTGGGCTTT-AAAAAAAATTGG
1 TGATAGGTGTCTGATTCTAACAAATTTGGTGCCACCAGTATTGGTGGGCTTTGAAAAAAGATTGG
2862576 GTGCCAC
66 GTGCCAC
2862583 TAACTCGTGT
Statistics
Matches: 184, Mismatches: 25, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
142 18 0.10
143 90 0.49
144 73 0.40
145 3 0.02
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (144 bp):
TGATAGGTGTCTGATTCTAACAAATTTGGTGCCACCAGTATTGGTGGGCTTTGAAAAAAGATTGG
GTGCCACCAGCTCATGTGGGCTTTTTAGAGAAAAGATTTAGAAGATTAAGATTTACTCCACAGGG
GATTGACACAACTA
Found at i:2863047 original size:12 final size:13
Alignment explanation
Indices: 2863016--2863072 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
2863006 GATGAAAGGC
2863016 TCTTGACACAAGT
1 TCTTGACACAAGT
2863029 TCTTGACA-AAGT
1 TCTTGACACAAGT
2863041 T-TCTGAC-CAACGT
1 TCT-TGACACAA-GT
* *
2863054 TCTCGACATAAGT
1 TCTTGACACAAGT
2863067 TCTTGA
1 TCTTGA
2863073 TGATAGTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
11 1 0.03
12 11 0.31
13 21 0.58
14 3 0.08
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (13 bp):
TCTTGACACAAGT
Found at i:2863055 original size:25 final size:26
Alignment explanation
Indices: 2863019--2863067 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
2863009 GAAAGGCTCT
*
2863019 TGACACAAGTTCTTGACA-AAGTTTC
1 TGACACAAGTTCTCGACATAAGTTTC
2863044 TGAC-CAACGTTCTCGACATAAGTT
1 TGACACAA-GTTCTCGACATAAGTT
2863068 CTTGATGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.62
26 5 0.24
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (26 bp):
TGACACAAGTTCTCGACATAAGTTTC
Found at i:2879675 original size:9 final size:9
Alignment explanation
Indices: 2879661--2879721 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
2879651 GGATGATAGG
2879661 AGGAGAGAT
1 AGGAGAGAT
2879670 AGGAGAGAT
1 AGGAGAGAT
*
2879679 AGTAGAGAT
1 AGGAGAGAT
*
2879688 AGGAG-GGT
1 AGGAGAGAT
* * *
2879696 -TGATAG-G
1 AGGAGAGAT
2879703 AGGAGAGAT
1 AGGAGAGAT
2879712 AGGAGAGAT
1 AGGAGAGAT
2879721 A
1 A
2879722 ATAAAGAGAT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 2 0.05
8 7 0.17
9 31 0.77
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:2879700 original size:42 final size:42
Alignment explanation
Indices: 2879651--2879753 Score: 143
Period size: 42 Copynumber: 2.4 Consensus size: 42
2879641 GAGATACAAA
* * *
2879651 GGATGATAGGAGGAGAGATAGGAGAGATAGTAGAGATAGGAG
1 GGATGATAGGAGGAGAGATAGGAGAGATAATAAAGAGAGGAG
* *
2879693 GGTTGATAGGAGGAGAGATAGGAGAGATAATAAAGAGATGAG
1 GGATGATAGGAGGAGAGATAGGAGAGATAATAAAGAGAGGAG
*
2879735 GGATGACAGGAGGACGAGA
1 GGATGATAGGAGGA-GAGA
2879754 GAAGAAGATG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 49 0.92
43 4 0.08
ACGTcount: A:0.41, C:0.02, G:0.44, T:0.14
Consensus pattern (42 bp):
GGATGATAGGAGGAGAGATAGGAGAGATAATAAAGAGAGGAG
Found at i:2880633 original size:45 final size:45
Alignment explanation
Indices: 2880584--2880719 Score: 119
Period size: 45 Copynumber: 3.1 Consensus size: 45
2880574 AGGACTTGGG
2880584 TTATTTTGTAATAATGGGCCTACTGGTTGTGACTTGCTTTGGGCT
1 TTATTTTGTAATAATGGGCCTACTGGTTGTGACTTGCTTTGGGCT
* * * *
2880629 TTA--TTG--AT-ATGGGCTCCAATGGAT-TGAATTAGGAC-TTGGG--
1 TTATTTTGTAATAATGGGC-CTACTGGTTGTGACTT--G-CTTTGGGCT
* *
2880669 TTATTTTGTAATAAAGGGTCTACTGGTTGTGACTTGCTTTGGGCT
1 TTATTTTGTAATAATGGGCCTACTGGTTGTGACTTGCTTTGGGCT
2880714 TTATTT
1 TTATTT
2880720 AGCATTAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 26
0.65 0.10 0.25
Matches are distributed among these distances:
40 14 0.21
41 8 0.12
42 10 0.15
43 10 0.15
44 8 0.12
45 18 0.26
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.43
Consensus pattern (45 bp):
TTATTTTGTAATAATGGGCCTACTGGTTGTGACTTGCTTTGGGCT
Found at i:2880692 original size:85 final size:85
Alignment explanation
Indices: 2880549--2880718 Score: 295
Period size: 85 Copynumber: 2.0 Consensus size: 85
2880539 ACGTTTGGAA
* *
2880549 GATATGGGCTCTAACAGATTGAATTAGGACTTGGGTTATTTTGTAATAATGGGCCTACTGGTTGT
1 GATATGGGCTCCAACAGATTGAATTAGGACTTGGGTTATTTTGTAATAAAGGGCCTACTGGTTGT
2880614 GACTTGCTTTGGGCTTTATT
66 GACTTGCTTTGGGCTTTATT
** *
2880634 GATATGGGCTCCAATGGATTGAATTAGGACTTGGGTTATTTTGTAATAAAGGGTCTACTGGTTGT
1 GATATGGGCTCCAACAGATTGAATTAGGACTTGGGTTATTTTGTAATAAAGGGCCTACTGGTTGT
2880699 GACTTGCTTTGGGCTTTATT
66 GACTTGCTTTGGGCTTTATT
2880719 TAGCATTAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.40
Consensus pattern (85 bp):
GATATGGGCTCCAACAGATTGAATTAGGACTTGGGTTATTTTGTAATAAAGGGCCTACTGGTTGT
GACTTGCTTTGGGCTTTATT
Found at i:2886583 original size:85 final size:85
Alignment explanation
Indices: 2886482--2886651 Score: 279
Period size: 85 Copynumber: 2.0 Consensus size: 85
2886472 ATATTTGGAA
* *
2886482 GATATGGGCTCCAATGGATTGAATTAGGACTTAGGTTATTTTGTAATAATGGGCCTACTGGTTGT
1 GATATGGGCTCCAATGGATTGAATTAGGACTTAGGTTATTTTGTAATAAAGAGCCTACTGGTTGT
2886547 GACTTGCTTTGGAG-TTTATT
66 GACTTGCTTTGG-GCTTTATT
* * *
2886567 GATATGGGTTCCAATGGATTGAATTAGGACTTGGGTTATTTTGTAATAAAGAGCCTGCTGGTTGT
1 GATATGGGCTCCAATGGATTGAATTAGGACTTAGGTTATTTTGTAATAAAGAGCCTACTGGTTGT
2886632 GACTTGCTTTGGGCTTTATT
66 GACTTGCTTTGGGCTTTATT
2886652 TAGCATAAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 1 0.01
85 78 0.99
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.40
Consensus pattern (85 bp):
GATATGGGCTCCAATGGATTGAATTAGGACTTAGGTTATTTTGTAATAAAGAGCCTACTGGTTGT
GACTTGCTTTGGGCTTTATT
Found at i:2903469 original size:20 final size:20
Alignment explanation
Indices: 2903444--2903485 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2903434 CTAGGCACTT
* *
2903444 CCAGGTCATAATCGGCCTAC
1 CCAGGTCACAATCGGCCAAC
*
2903464 CCAGGTCACAATTGGCCAAC
1 CCAGGTCACAATCGGCCAAC
2903484 CC
1 CC
2903486 CCACACCTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.38, G:0.19, T:0.17
Consensus pattern (20 bp):
CCAGGTCACAATCGGCCAAC
Found at i:2905674 original size:20 final size:19
Alignment explanation
Indices: 2905651--2905703 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
2905641 CACACCCAGA
2905651 TGTATCGATACATATTGCTT
1 TGTATCGATACATATT-CTT
*
2905671 TGTATCGATACATGTTCTT
1 TGTATCGATACATATTCTT
* *
2905690 GGTATCAATACATA
1 TGTATCGATACATA
2905704 GTAAATTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATATTCTT
Found at i:2905700 original size:19 final size:20
Alignment explanation
Indices: 2905652--2905703 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
2905642 ACACCCAGAT
*
2905652 GTATCGATACATATTGCTTT
1 GTATCGATACATATTGCTTG
*
2905672 GTATCGATACATGTT-CTTG
1 GTATCGATACATATTGCTTG
*
2905691 GTATCAATACATA
1 GTATCGATACATA
2905704 GTAAATTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
GTATCGATACATATTGCTTG
Found at i:2911356 original size:12 final size:12
Alignment explanation
Indices: 2911341--2911384 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
2911331 TCTATTATCT
2911341 CTCCTATCATCC
1 CTCCTATCATCC
2911353 CTCCTATC-TCTC
1 CTCCTATCATC-C
2911365 CTCCTATCATCC
1 CTCCTATCATCC
2911377 CTCCTATC
1 CTCCTATC
2911385 TCTTCTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.07
12 26 0.87
13 2 0.07
ACGTcount: A:0.14, C:0.50, G:0.00, T:0.36
Consensus pattern (12 bp):
CTCCTATCATCC
Found at i:2911368 original size:24 final size:24
Alignment explanation
Indices: 2911341--2911387 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2911331 TCTATTATCT
2911341 CTCCTATCATCCCTCCTATCTCTC
1 CTCCTATCATCCCTCCTATCTCTC
2911365 CTCCTATCATCCCTCCTATCTCT
1 CTCCTATCATCCCTCCTATCTCT
2911388 TCTTTCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.13, C:0.49, G:0.00, T:0.38
Consensus pattern (24 bp):
CTCCTATCATCCCTCCTATCTCTC
Found at i:2918983 original size:21 final size:20
Alignment explanation
Indices: 2918957--2918995 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2918947 AGGTCAAAAC
2918957 CCTAGAAAGTATCGATACACA
1 CCTAG-AAGTATCGATACACA
*
2918978 CCTAGATGTATCGATACA
1 CCTAGAAGTATCGATACA
2918996 TATTGCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CCTAGAAGTATCGATACACA
Found at i:2923936 original size:103 final size:103
Alignment explanation
Indices: 2923739--2923967 Score: 305
Period size: 103 Copynumber: 2.2 Consensus size: 103
2923729 TATCAAAATT
* * * * * *
2923739 TTATTCACAGGGACACTCCAACCCTGACCTTTCGAGGGAATACTCCAATCCCATTGTTCAAAAAT
1 TTATCCACGGGGATACTCCAACCCTAACCTTTCGAGGGAATACTCCAATCCCACTCTTCAAAAAT
* *
2923804 TATCTAGATTTGAACTCCTCCTTTCTCAAAATTATTTG
66 TATCAAGATCTGAACTCCTCCTTTCTCAAAATTATTTG
* * * * *
2923842 TTATCTATGGGGATACTCCAACCCTAACCTTTCGAGGGGATACTCCAATCTCACTCTTCAAAATT
1 TTATCCACGGGGATACTCCAACCCTAACCTTTCGAGGGAATACTCCAATCCCACTCTTCAAAAAT
* ** *
2923907 TATCAAGATCTGAACTCTTTTTTTGTCAAAATTATTTG
66 TATCAAGATCTGAACTCCTCCTTTCTCAAAATTATTTG
2923945 TTATCCACGGGGATACTCCAACC
1 TTATCCACGGGGATACTCCAACC
2923968 TCATCTTCCA
Statistics
Matches: 107, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (103 bp):
TTATCCACGGGGATACTCCAACCCTAACCTTTCGAGGGAATACTCCAATCCCACTCTTCAAAAAT
TATCAAGATCTGAACTCCTCCTTTCTCAAAATTATTTG
Found at i:2927765 original size:5 final size:5
Alignment explanation
Indices: 2927755--2927779 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2927745 TGGAAAAAAC
2927755 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
2927780 TCCAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:2929514 original size:85 final size:82
Alignment explanation
Indices: 2929425--2929854 Score: 321
Period size: 85 Copynumber: 5.1 Consensus size: 82
2929415 AAGCAGTCAG
* * *
2929425 GTCAACAAAGTATGAAAGAGGTTACCTGGGACTAAACCGACAGGTAAACAAGGGATACAAAAGTT
1 GTCAACAAAGGAT-AAAGAGGTTACCTGGGACTAAGCCGACAGGTAAACAAAGGATA-AAAAGTT
* *
2929490 GATCGAGATTGAATCGACAA
64 GA-CGAGATTGAACCAACAA
* ** * * * * *
2929510 GTCAACAAAGGATAAAAAAATTTACCTGGGACTAAGCTGACGGGTAGACAAGGGATGAAAGAGTT
1 GTCAACAAAGGAT-AAAGAGGTTACCTGGGACTAAGCCGACAGGTAAACAAAGGAT-AAAAAGTT
* * *
2929575 GAACGGGGTTGAATCAACAA
64 G-ACGAGATTGAACCAACAA
* * * * *
2929595 GTCAATAATA-GATAAATGA-TTTACCTAGGACTAAGCCGACAAGTAAACAAAGGAAAAAAAGGT
1 GTCAACAA-AGGATAAA-GAGGTTACCTGGGACTAAGCCGACAGGTAAACAAAGGATAAAAA-GT
* *
2929658 TGACCAGGATTGAACCGACAA
63 TGACGA-GATTGAACCAACAA
* ** * *
2929679 GTCGACAAAGGATAAA-AGGATTTA-CTCGGGACTAAGCTAATAGGTAAACAAAGGATTAAAAGG
1 GTCAACAAAGGATAAAGAGG--TTACCT-GGGACTAAGCCGACAGGTAAACAAAGGA-TAAAAAG
2929742 TTGACTGAGATTGAACCAACAA
62 TTGAC-GAGATTGAACCAACAA
* ** * * *
2929764 GTCAACAAAGGGTAAA-AGGATTTGCTCGGGATTAAGCTGACATGTAAACAAAGGATAAAAAGGT
1 GTCAACAAAGGATAAAGAGG-TTACCT-GGGACTAAGCCGACAGGTAAACAAAGGATAAAAA-GT
* * *
2929828 TGATAGGGATTGAACTAACAA
63 TGA-CGAGATTGAACCAACAA
2929849 GTCAAC
1 GTCAAC
2929855 CAATTGAAGG
Statistics
Matches: 277, Mismatches: 52, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
82 1 0.00
83 7 0.03
84 68 0.25
85 193 0.70
86 8 0.03
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (82 bp):
GTCAACAAAGGATAAAGAGGTTACCTGGGACTAAGCCGACAGGTAAACAAAGGATAAAAAGTTGA
CGAGATTGAACCAACAA
Found at i:2929732 original size:43 final size:43
Alignment explanation
Indices: 2929683--2929823 Score: 144
Period size: 43 Copynumber: 3.3 Consensus size: 43
2929673 CGACAAGTCG
* * *
2929683 ACAAAGGATAAAAGGATTTACTCGGGACTAAGCTAATAGGTAA
1 ACAAAGGATAAAAGGATTTACTCGGGATTAAGCTAACAAGTAA
* * * *
2929726 ACAAAGGATTAAAAGG-TTGACT-GAGATTGAA-CCAACAAGTCA
1 ACAAAGGA-TAAAAGGATTTACTCGGGATT-AAGCTAACAAGTAA
* * * *
2929768 ACAAAGGGTAAAAGGATTTGCTCGGGATTAAGCTGACATGTAA
1 ACAAAGGATAAAAGGATTTACTCGGGATTAAGCTAACAAGTAA
2929811 ACAAAGGATAAAA
1 ACAAAGGATAAAA
2929824 AGGTTGATAG
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
41 7 0.09
42 24 0.31
43 39 0.51
44 7 0.09
ACGTcount: A:0.45, C:0.12, G:0.23, T:0.20
Consensus pattern (43 bp):
ACAAAGGATAAAAGGATTTACTCGGGATTAAGCTAACAAGTAA
Found at i:2929764 original size:169 final size:170
Alignment explanation
Indices: 2929425--2929854 Score: 412
Period size: 169 Copynumber: 2.5 Consensus size: 170
2929415 AAGCAGTCAG
* * * * *
2929425 GTCAACAAAGTATGAAAGAGG--TTACCTGGGACTAAACCGACAGGTAAACAAGGGATACAAAA-
1 GTCAACAAAGGAT-AAA-AGGATTTACCTGGGACTAAGCCGACAAGTAAACAAAGGA-AAAAAAG
* * * *
2929487 GTTGATCGAGATTGAATCGACAAGTCAACAAAGGATAAAAAAATTTACCTGGGACTAAGCTGACG
63 GTTGACCGAGATTGAACCGACAAGTCAACAAAGGATAAAAAAATTTACCTGGGACTAAGCTAACA
* * * * * *
2929552 GGTAGACAAGGGATGAAAGAGTTGAACGGGGTTGAATCAACAA
128 GGTAAACAAAGGATAAAAGAGTTGAACGAGATTGAACCAACAA
* * *
2929595 GTCAATAATA-GAT-AAATGATTTACCTAGGACTAAGCCGACAAGTAAACAAAGGAAAAAAAGGT
1 GTCAACAA-AGGATAAAAGGATTTACCTGGGACTAAGCCGACAAGTAAACAAAGGAAAAAAAGGT
* ** *
2929658 TGACC-AGGATTGAACCGACAAGTCGACAAAGGATAAAAGGATTTA-CTCGGGACTAAGCTAATA
65 TGACCGA-GATTGAACCGACAAGTCAACAAAGGATAAAAAAATTTACCT-GGGACTAAGCTAACA
2929721 GGTAAACAAAGGATTAAAAG-GTTG-ACTGAGATTGAACCAACAA
128 GGTAAACAAAGGA-TAAAAGAGTTGAAC-GAGATTGAACCAACAA
* * * * * *
2929764 GTCAACAAAGGGTAAAAGGATTT-GCTCGGGATTAAGCTGACATGTAAACAAAGGATAAAAAGGT
1 GTCAACAAAGGATAAAAGGATTTACCT-GGGACTAAGCCGACAAGTAAACAAAGGAAAAAAAGGT
** * **
2929828 TGATAGGGATTGAACTAACAAGTCAAC
65 TGACCGAGATTGAACCGACAAGTCAAC
2929855 CAATTGAAGG
Statistics
Matches: 211, Mismatches: 37, Indels: 24
0.78 0.14 0.09
Matches are distributed among these distances:
167 2 0.01
168 13 0.06
169 121 0.57
170 74 0.35
171 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (170 bp):
GTCAACAAAGGATAAAAGGATTTACCTGGGACTAAGCCGACAAGTAAACAAAGGAAAAAAAGGTT
GACCGAGATTGAACCGACAAGTCAACAAAGGATAAAAAAATTTACCTGGGACTAAGCTAACAGGT
AAACAAAGGATAAAAGAGTTGAACGAGATTGAACCAACAA
Found at i:2930131 original size:46 final size:46
Alignment explanation
Indices: 2929972--2930132 Score: 178
Period size: 46 Copynumber: 3.5 Consensus size: 46
2929962 CCGATAAAAC
* * * * *
2929972 CAAACGAGAATGAAAAGGGTTTGACCAGAGTGGTAATTGATACAAT
1 CAAACAAGAATGAAAAAGGTTTGACCAGGGTGGTAACTGATACAGT
* * * * * * *
2930018 CAAATAAGAATAAAAAAGGTTAGACCATGATGATAACTGATGCAGT
1 CAAACAAGAATGAAAAAGGTTTGACCAGGGTGGTAACTGATACAGT
* * *
2930064 CAAACAAGGATGAAAAAGGTTTGACTAGGGTGGTAACTGATACCGT
1 CAAACAAGAATGAAAAAGGTTTGACCAGGGTGGTAACTGATACAGT
*
2930110 CAAACGAGAATGAAAAAGGTTTG
1 CAAACAAGAATGAAAAAGGTTTG
2930133 TTTGGTAAAT
Statistics
Matches: 91, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
46 91 1.00
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (46 bp):
CAAACAAGAATGAAAAAGGTTTGACCAGGGTGGTAACTGATACAGT
Found at i:2930933 original size:78 final size:77
Alignment explanation
Indices: 2930764--2930947 Score: 237
Period size: 78 Copynumber: 2.4 Consensus size: 77
2930754 ATCTAACGGA
* * *
2930764 TGAATGAAGGAGATATGATTGGGAATGTGTAGGCTACACCTTTTGTGGTCATGTGATGCATCAAT
1 TGAATGAAGGAGATATAATT-GGAATGTGTAGGCCACACCTTTTGTGGTAATGTGATGCATCAAT
2930829 ATCATCTAGTAAC
65 ATCATCTAGTAAC
* * *
2930842 TGAAAGAAGGAGATATAATTGGCAATGTGTGGGCCACACCTTTTGTGGTAATGTGATGCA-CTTA
1 TGAATGAAGGAGATATAATTGG-AATGTGTAGGCCACACCTTTTGTGGTAATGTGATGCATC-AA
*
2930906 TATCATCTAGTGAC
64 TATCATCTAGTAAC
*
2930920 TGAATGGAA-GAGATACAATTAGGAATGT
1 TGAAT-GAAGGAGATATAATT-GGAATGT
2930948 ATGGTTGGGA
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
77 3 0.03
78 85 0.91
79 5 0.05
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (77 bp):
TGAATGAAGGAGATATAATTGGAATGTGTAGGCCACACCTTTTGTGGTAATGTGATGCATCAATA
TCATCTAGTAAC
Found at i:2931785 original size:27 final size:27
Alignment explanation
Indices: 2931755--2931812 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
2931745 CTTATTCGGG
*
2931755 TTTTCATCCCATTTTTTATCTTT-TTGA
1 TTTTCATACCATTTTTTAT-TTTATTGA
** *
2931782 TTTTTTTACGATTTTTTATTTTATTGA
1 TTTTCATACCATTTTTTATTTTATTGA
2931809 TTTT
1 TTTT
2931813 ATTGATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.16, C:0.10, G:0.05, T:0.69
Consensus pattern (27 bp):
TTTTCATACCATTTTTTATTTTATTGA
Found at i:2931787 original size:9 final size:9
Alignment explanation
Indices: 2931766--2931832 Score: 61
Period size: 9 Copynumber: 7.7 Consensus size: 9
2931756 TTTCATCCCA
2931766 TTTTTT-AT
1 TTTTTTGAT
*
2931774 CTTTTTGAT
1 TTTTTTGAT
2931783 TTTTTTACGA-
1 TTTTTT--GAT
2931793 TTTTTT-AT
1 TTTTTTGAT
*
2931801 TTTATTGAT
1 TTTTTTGAT
*
2931810 TTTATTGAT
1 TTTTTTGAT
2931819 TTTTTTG-T
1 TTTTTTGAT
2931827 TTTTTT
1 TTTTTT
2931833 TACACGTAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
7 1 0.02
8 17 0.34
9 24 0.48
10 6 0.12
11 2 0.04
ACGTcount: A:0.13, C:0.03, G:0.07, T:0.76
Consensus pattern (9 bp):
TTTTTTGAT
Found at i:2932926 original size:13 final size:13
Alignment explanation
Indices: 2932908--2932933 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2932898 TACACCAAGT
2932908 ATGTATCGATACA
1 ATGTATCGATACA
2932921 ATGTATCGATACA
1 ATGTATCGATACA
2932934 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2932931 original size:32 final size:33
Alignment explanation
Indices: 2932890--2932953 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2932880 TAGCCAAACT
* **
2932890 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2932922 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2932954 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2935184 original size:21 final size:21
Alignment explanation
Indices: 2935151--2935200 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
2935141 TTGCAAGTTG
*
2935151 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2935173 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
2935194 AAATAAA
1 AAATAAA
2935201 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2937018 original size:15 final size:15
Alignment explanation
Indices: 2936998--2937028 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2936988 TAAAAATGTC
*
2936998 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2937013 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2937028 C
1 C
2937029 CACAAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2939115 original size:13 final size:13
Alignment explanation
Indices: 2939097--2939135 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
2939087 ACATTTTTCT
2939097 TTGTATCGATACA
1 TTGTATCGATACA
2939110 TTGTATCGATACA
1 TTGTATCGATACA
2939123 TTGTATCGATACA
1 TTGTATCGATACA
2939136 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2939299 original size:20 final size:20
Alignment explanation
Indices: 2939256--2939301 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2939246 AAATCTTTTG
2939256 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
2939277 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
2939297 CAAAA
1 CAAAA
2939302 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:2941696 original size:13 final size:13
Alignment explanation
Indices: 2941678--2941703 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2941668 TACACGAAGT
2941678 ATGTATCGATACA
1 ATGTATCGATACA
2941691 ATGTATCGATACA
1 ATGTATCGATACA
2941704 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2941701 original size:32 final size:33
Alignment explanation
Indices: 2941660--2941723 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2941650 TAGCCAAACT
* **
2941660 TGTATCGATACACGAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2941692 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2941724 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2945413 original size:33 final size:32
Alignment explanation
Indices: 2945371--2945434 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
2945361 CACACCCAGA
2945371 TGTATCGATACATATTGCTTAGTATCAATACAT
1 TGTATCGATACATATT-CTTAGTATCAATACAT
* * *
2945404 TGTATCGATACATGTTCTTGGTATCGATACA
1 TGTATCGATACATATTCTTAGTATCAATACA
2945435 CATGACTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATATTCTTAGTATCAATACAT
Found at i:2945446 original size:19 final size:20
Alignment explanation
Indices: 2945403--2945453 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
2945393 TATCAATACA
*
2945403 TTGTATCGAT--ACATGTTC
1 TTGTATCGATACACATGTAC
2945421 TTGGTATCGATACACATG-AC
1 TT-GTATCGATACACATGTAC
*
2945441 TTGTATTGATACA
1 TTGTATCGATACA
2945454 TGAAACTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.07
19 18 0.64
20 3 0.11
21 5 0.18
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACACATGTAC
Found at i:2951137 original size:36 final size:32
Alignment explanation
Indices: 2951054--2951149 Score: 108
Period size: 36 Copynumber: 3.0 Consensus size: 32
2951044 CCTTACAACA
2951054 CTATC-TTTC-AAGGCTAAGATAGAAACCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAAACCTCC
** *
2951084 CTATCTTTTCACGGGCTAAGATAGAATGTCTCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAA--AC-CTCC
2951119 CTATCTTTTTCAAAGGCTAAGATAG-AACCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAAACCTC
2951150 TCAATCACTT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
30 5 0.09
31 4 0.07
32 16 0.30
33 1 0.02
34 1 0.02
35 10 0.19
36 17 0.31
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (32 bp):
CTATCTTTTCAAAGGCTAAGATAGAAACCTCC
Found at i:2956686 original size:20 final size:19
Alignment explanation
Indices: 2956660--2956710 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2956650 CTGCCAGTTT
*
2956660 CATGTATCGATACATTTG-G
1 CATGTATCGATACA-ATGAG
*
2956679 CTATGTATCAATACAATGAG
1 C-ATGTATCGATACAATGAG
2956699 CATGTATCGATA
1 CATGTATCGATA
2956711 TAAAGCATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:2956850 original size:38 final size:38
Alignment explanation
Indices: 2956799--2956913 Score: 203
Period size: 38 Copynumber: 3.0 Consensus size: 38
2956789 TAATGTATCG
*
2956799 ATACAAATACCTATGTATCAATACTATGAATTATTTTT
1 ATACAAATACCTATGTATCGATACTATGAATTATTTTT
*
2956837 ATACAAATACCTATGTATTGATACTATGAATTATTTTT
1 ATACAAATACCTATGTATCGATACTATGAATTATTTTT
*
2956875 ATACAAATACCTATGTATCGATGCTATGAATTATTTTT
1 ATACAAATACCTATGTATCGATACTATGAATTATTTTT
2956913 A
1 A
2956914 CTTAAAAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 73 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (38 bp):
ATACAAATACCTATGTATCGATACTATGAATTATTTTT
Found at i:2957304 original size:141 final size:140
Alignment explanation
Indices: 2957149--2957411 Score: 404
Period size: 141 Copynumber: 1.9 Consensus size: 140
2957139 GATACGAAAT
* *
2957149 GTTTTGAAAATTTCTATACCTTTACG-AAAACCATAAGAATATTAGAAAAT-CTTAAAAAATTAA
1 GTTTTGAAAATTTCTATACCCTTACGAAAAACCATAAGAATATTAG-AAATCCTGAAAAAA-TAA
*
2957212 GATAATAATTTTTATTTAATTTTTTAATTTCTAAAAAATTCATTTCATACCCTAATGGAGAACCG
64 GATAATAATTTTTATTTAATTTTTTAATTTCTAAAAAATTCATTT-ATACCCTAAAGGAGAACCG
2957277 AAAAGATACAATA
128 AAAAGATACAATA
* * *
2957290 GTTTTGAAGATTTCTATACCCTTATGAAAAACCATAGGAATATTAGAAATCCTGAAAAAATAAGA
1 GTTTTGAAAATTTCTATACCCTTACGAAAAACCATAAGAATATTAGAAATCCTGAAAAAATAAGA
* * *
2957355 TAATAATTTTTATTTAATTTTTTCATTTCTAAAAAATTTATTTATACCTTAAAGGAG
66 TAATAATTTTTATTTAATTTTTTAATTTCTAAAAAATTCATTTATACCCTAAAGGAG
2957412 GACTAAAAAG
Statistics
Matches: 111, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
140 12 0.11
141 73 0.66
142 26 0.23
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (140 bp):
GTTTTGAAAATTTCTATACCCTTACGAAAAACCATAAGAATATTAGAAATCCTGAAAAAATAAGA
TAATAATTTTTATTTAATTTTTTAATTTCTAAAAAATTCATTTATACCCTAAAGGAGAACCGAAA
AGATACAATA
Found at i:2958396 original size:10 final size:10
Alignment explanation
Indices: 2958381--2958429 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
2958371 TCCTAACTAG
*
2958381 TTTTTCTATT
1 TTTTTCTCTT
2958391 TTTTTCT-TT
1 TTTTTCTCTT
2958400 TTTCTTCTCTT
1 TTT-TTCTCTT
2958411 TTTTTCTCTCT
1 TTTTTCTCT-T
2958422 TTTTTCTC
1 TTTTTCTC
2958430 CCTTGCCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.14
10 17 0.47
11 14 0.39
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:2958412 original size:12 final size:13
Alignment explanation
Indices: 2958395--2958429 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
2958385 TCTATTTTTT
2958395 TCTTTTTTCT-TC
1 TCTTTTTTCTCTC
2958407 TCTTTTTT-TCTC
1 TCTTTTTTCTCTC
2958419 TCTTTTTTCTC
1 TCTTTTTTCTC
2958430 CCTTGCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 18 0.86
13 2 0.10
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TCTTTTTTCTCTC
Found at i:2960675 original size:170 final size:170
Alignment explanation
Indices: 2960416--2960845 Score: 440
Period size: 170 Copynumber: 2.5 Consensus size: 170
2960406 AAGCAGTCAG
* * * * * * *
2960416 GTCAACAAAGTATGAAAGGGA-TTACCTGGGACTAA-ATCAATAGGTAAACAAGGGATACAAAA-
1 GTCAACAAAGGAT-AAAGGGATTTACCAGAGACTAAGCT-GATAGGTAAACAAAGGA-AAAAAAG
* * *
2960478 GTTAACTAAGATTGAGCTAACAAGTCAATAAAAGGATAAAAGGATTTACCCAAGACTAAGTTGAC
63 GTTGACTAAGATTGAACTAACAAGTCAA-AAAAGGATAAAAGGATTTACCCAAGACTAAGCTGAC
* * ** ** *
2960543 GGGT-AGACAAGGGAT-GGAAGAGTTGACCGGGATTGAACCGATAA
127 AGGTAAG-CAAAGGATAAAAAG-GTTGACCAAGATTGAACCGACAA
* *
2960587 GTCAACAAAGGATAAA-TGATTTACCCGAGACTAAGCTGATAGGTAAACAAAGGAAAAAAAGGTT
1 GTCAACAAAGGATAAAGGGATTTACCAGAGACTAAGCTGATAGGTAAACAAAGGAAAAAAAGGTT
* * * * * *
2960651 GATTGAGATTGAACTCACAAGTCAACAAAGGATAAAAGGATTTACCTAGGACTAAGCTGACAGGT
66 GACTAAGATTGAACTAACAAGTCAAAAAAGGATAAAAGGATTTACCCAAGACTAAGCTGACAGGT
*
2960716 AAGCAAAGGATAAAAAGGTTTACCAAGATTGAACCGACAA
131 AAGCAAAGGATAAAAAGGTTGACCAAGATTGAACCGACAA
** * * * * *
2960756 GTTGACAAAGGATAAAGGGATTTACCAGTGATTAAGGTGATAGCTAAACAAAGGATAAAAAGGTT
1 GTCAACAAAGGATAAAGGGATTTACCAGAGACTAAGCTGATAGGTAAACAAAGGAAAAAAAGGTT
* * *
2960821 GACTAGGATTTAACCAACAAGTCAA
66 GACTAAGATTGAACTAACAAGTCAA
2960846 CCAATTGGAT
Statistics
Matches: 213, Mismatches: 40, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
169 82 0.38
170 118 0.55
171 13 0.06
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (170 bp):
GTCAACAAAGGATAAAGGGATTTACCAGAGACTAAGCTGATAGGTAAACAAAGGAAAAAAAGGTT
GACTAAGATTGAACTAACAAGTCAAAAAAGGATAAAAGGATTTACCCAAGACTAAGCTGACAGGT
AAGCAAAGGATAAAAAGGTTGACCAAGATTGAACCGACAA
Found at i:2960724 original size:85 final size:85
Alignment explanation
Indices: 2960497--2960846 Score: 325
Period size: 85 Copynumber: 4.1 Consensus size: 85
2960487 GATTGAGCTA
* * * * * ***
2960497 ACAAGTCAATAAAAGGATAAAAGGATTTACCCA-AGACTAAGTTGACGGGTAGAC-AAGGGATGG
1 ACAAGTCAA-CAAAGGATAAAAGGATTTA-CCAGAGACTAAGCTGACAGGTAAACAAAGGAAAAA
*
2960560 AAGAGTTGACCGGGATTGAACCG
64 AAG-GTTGACCGAGATTGAACCG
* * * *
2960583 ATAAGTCAACAAAGGAT-AAATGATTTACCCGAGACTAAGCTGATAGGTAAACAAAGGAAAAAAA
1 ACAAGTCAACAAAGGATAAAAGGATTTACCAGAGACTAAGCTGACAGGTAAACAAAGGAAAAAAA
**
2960647 GGTTGATTGAGATTGAACTC-
66 GGTTGACCGAGATTGAAC-CG
* *
2960667 ACAAGTCAACAAAGGATAAAAGGATTTACCTAG-GACTAAGCTGACAGGTAAGCAAAGGATAAAA
1 ACAAGTCAACAAAGGATAAAAGGATTTACC-AGAGACTAAGCTGACAGGTAAACAAAGGAAAAAA
* *
2960731 AGGTTTACCAAGATTGAACCG
65 AGGTTGACCGAGATTGAACCG
** * * * * * * *
2960752 ACAAGTTGACAAAGGATAAAGGGATTTACCAGTGATTAAGGTGATAGCTAAACAAAGGATAAAAA
1 ACAAGTCAACAAAGGATAAAAGGATTTACCAGAGACTAAGCTGACAGGTAAACAAAGGAAAAAAA
* * *
2960817 GGTTGA-CTAGGATTTAACCA
66 GGTTGACCGA-GATTGAACCG
2960837 ACAAGTCAAC
1 ACAAGTCAAC
2960847 CAATTGGATG
Statistics
Matches: 217, Mismatches: 39, Indels: 17
0.79 0.14 0.06
Matches are distributed among these distances:
83 2 0.01
84 61 0.28
85 145 0.67
86 9 0.04
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.19
Consensus pattern (85 bp):
ACAAGTCAACAAAGGATAAAAGGATTTACCAGAGACTAAGCTGACAGGTAAACAAAGGAAAAAAA
GGTTGACCGAGATTGAACCG
Found at i:2961036 original size:46 final size:46
Alignment explanation
Indices: 2960976--2961170 Score: 243
Period size: 46 Copynumber: 4.2 Consensus size: 46
2960966 AATAAGAACA
* * *
2960976 AAAAGGGTTTGACCAGGGTGGTAACTAATACAATCAAAC-AAGAATG
1 AAAAGGGTTTGACCAGGGTGATAACTGATACAGTCAAACAAAG-ATG
2961022 AAAAGGGTTTGACCAGGGTGATAACTGATACAGTCAAACAAAGATG
1 AAAAGGGTTTGACCAGGGTGATAACTGATACAGTCAAACAAAGATG
* * *
2961068 AAAATGGTTTAACCAGGGTGATAACCGATACAGTCAAACAAAGATG
1 AAAAGGGTTTGACCAGGGTGATAACTGATACAGTCAAACAAAGATG
* * * * *
2961114 AAAAGGGTTTGACTAGGGTGGT-AGTCGACACAGTCAAAC-GAGAATG
1 AAAAGGGTTTGACCAGGGTGATAACT-GATACAGTCAAACAAAG-ATG
2961160 AAAAGGGTTTG
1 AAAAGGGTTTG
2961171 TTTGGTAAAT
Statistics
Matches: 132, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
45 3 0.02
46 126 0.95
47 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.27, T:0.20
Consensus pattern (46 bp):
AAAAGGGTTTGACCAGGGTGATAACTGATACAGTCAAACAAAGATG
Found at i:2962746 original size:8 final size:8
Alignment explanation
Indices: 2962733--2962780 Score: 69
Period size: 8 Copynumber: 5.8 Consensus size: 8
2962723 TCGTTCGATA
*
2962733 TTTTTTGT
1 TTTTTTAT
2962741 TTTTTTAT
1 TTTTTTAT
2962749 TTTTTTAT
1 TTTTTTAT
2962757 TTTTTTGAT
1 TTTTTT-AT
2962766 TTTTTTAAT
1 TTTTTT-AT
2962775 TTTTTT
1 TTTTTT
2962781 TACATATAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
8 21 0.57
9 16 0.43
ACGTcount: A:0.10, C:0.00, G:0.04, T:0.85
Consensus pattern (8 bp):
TTTTTTAT
Done.