Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 139 of 173
Found at i:42278689 original size:24 final size:24
Alignment explanation
Indices: 42278657--42278706 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
42278647 TAGCCTGACC
* *
42278657 TATTTTAAAGTTTATA-ATATTTTA
1 TATTATAAA-TTTATATATATTATA
*
42278681 TATTATAAATTTTTATATATTATA
1 TATTATAAATTTATATATATTATA
42278705 TA
1 TA
42278707 ATTTATAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TATTATAAATTTATATATATTATA
Found at i:42279288 original size:82 final size:82
Alignment explanation
Indices: 42279138--42279289 Score: 202
Period size: 82 Copynumber: 1.9 Consensus size: 82
42279128 GTTGTTTTTT
* *
42279138 TATTCCCTCATAAATTTTGATACACACCTTATAATTTTTTATATTCCCCATGTTTTTTTTGCACT
1 TATTCCCTCATAAATTTTGATACACACCTCATAATTTTTTATATTCCCCATGTTTTTTTTACACT
42279203 TCCTCGGATTATTTTGG
66 TCCTCGGATTATTTTGG
* * *
42279220 TATT-CCTCTTAAATTTTTGGTACA-AGCCTCATAATTTTTTATACTTCCCCAT-TTTTTTTTAT
1 TATTCCCTCATAAA-TTTTGATACACA-CCTCATAATTTTTTATA-TTCCCCATGTTTTTTTTAC
*
42279282 ATTTCCTC
63 ACTTCCTC
42279290 ATAATTTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
81 9 0.15
82 44 0.72
83 8 0.13
ACGTcount: A:0.22, C:0.21, G:0.07, T:0.51
Consensus pattern (82 bp):
TATTCCCTCATAAATTTTGATACACACCTCATAATTTTTTATATTCCCCATGTTTTTTTTACACT
TCCTCGGATTATTTTGG
Found at i:42279297 original size:20 final size:20
Alignment explanation
Indices: 42279246--42279316 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
42279236 TTGGTACAAG
42279246 CCTCATAATTTTTTATACTT
1 CCTCATAATTTTTTATACTT
* ** *
42279266 CCCCATTTTTTTTTATATTT
1 CCTCATAATTTTTTATACTT
* *
42279286 CCTCATAATTTTTTACACTC
1 CCTCATAATTTTTTATACTT
42279306 CCTCAT-ATTTT
1 CCTCATAATTTT
42279317 ATGGTATGCT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
19 5 0.12
20 36 0.88
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (20 bp):
CCTCATAATTTTTTATACTT
Found at i:42279354 original size:20 final size:21
Alignment explanation
Indices: 42279307--42279356 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
42279297 TTTACACTCC
42279307 CTCAT-ATTTTATGGTATGCT
1 CTCATAATTTTATGGTATGCT
* *
42279327 CTCCTAATTTT-TGGTATTCT
1 CTCATAATTTTATGGTATGCT
*
42279347 TTCATAATTT
1 CTCATAATTT
42279357 GTTTTGCATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.20, C:0.16, G:0.10, T:0.54
Consensus pattern (21 bp):
CTCATAATTTTATGGTATGCT
Found at i:42279786 original size:20 final size:20
Alignment explanation
Indices: 42279753--42279845 Score: 55
Period size: 20 Copynumber: 4.6 Consensus size: 20
42279743 AAAAACATTG
** *
42279753 GGGATTACTTAAAAATATGA
1 GGGATTACCAAAAAATACGA
42279773 GGGATTACC-AAAAATAACGA
1 GGGATTACCAAAAAAT-ACGA
** * *
42279793 GGGCGT-GCAAAAAATTACGT
1 GGGATTACCAAAAAA-TACGA
* *
42279813 GAGATTACCAAAAAAATATGA
1 GGGATTACC-AAAAAATACGA
*
42279834 GGGACTACCAAA
1 GGGATTACCAAA
42279846 TATTGGCTCG
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
19 7 0.13
20 29 0.54
21 12 0.22
22 6 0.11
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.19
Consensus pattern (20 bp):
GGGATTACCAAAAAATACGA
Found at i:42280842 original size:48 final size:49
Alignment explanation
Indices: 42280773--42280865 Score: 152
Period size: 48 Copynumber: 1.9 Consensus size: 49
42280763 GCATGATTTT
* * *
42280773 TTTTATCTTGAGGCGTGAATCATTTTCCTTATCGCTTTATCTTTTTTCG
1 TTTTATCTTGAGGCGTAAATCACTTTCCATATCGCTTTATCTTTTTTCG
42280822 TTTTAT-TTGAGGCGTAAATCACTTTCCATATCGCTTTATCTTTT
1 TTTTATCTTGAGGCGTAAATCACTTTCCATATCGCTTTATCTTTT
42280866 GACCGATGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 35 0.85
49 6 0.15
ACGTcount: A:0.17, C:0.18, G:0.13, T:0.52
Consensus pattern (49 bp):
TTTTATCTTGAGGCGTAAATCACTTTCCATATCGCTTTATCTTTTTTCG
Found at i:42286879 original size:21 final size:21
Alignment explanation
Indices: 42286853--42286893 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42286843 AGACGAGCAA
* *
42286853 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
42286874 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
42286894 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:42291314 original size:3 final size:3
Alignment explanation
Indices: 42291306--42291341 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
42291296 CTGAAAATTG
42291306 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42291342 GAAACTCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:42292003 original size:29 final size:29
Alignment explanation
Indices: 42291971--42292034 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
42291961 AAAATTTTTA
* *
42291971 TTAAGTCACTAAATTATCT-AAAAAATTAT
1 TTAAGTCACGAAACTAT-TAAAAAAATTAT
*
42292000 TTAAGTTACGAAACTATTAAAAAAATTAT
1 TTAAGTCACGAAACTATTAAAAAAATTAT
42292029 TTAAGT
1 TTAAGT
42292035 TATTGGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (29 bp):
TTAAGTCACGAAACTATTAAAAAAATTAT
Found at i:42294121 original size:22 final size:23
Alignment explanation
Indices: 42294094--42294138 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
42294084 AGGTATCTAC
42294094 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
42294116 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
42294139 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:42294142 original size:17 final size:17
Alignment explanation
Indices: 42294120--42294172 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 17
42294110 ATTACAAAAT
42294120 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
* *
42294137 CATATCATATCTATGATTG
1 CATATC-T-TCTAAGATTA
* *
42294156 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
42294173 TGTTTCCATA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 13 0.46
18 1 0.04
19 14 0.50
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:42294143 original size:22 final size:22
Alignment explanation
Indices: 42294091--42294148 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
42294081 GAAAGGTATC
*
42294091 TACAAATCAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
42294112 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
42294135 TACATATCATATCT
1 TACAAATCATATCT
42294149 ATGATTGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 19 0.58
23 11 0.33
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.34
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:42300185 original size:22 final size:23
Alignment explanation
Indices: 42300158--42300202 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
42300148 AGGTATCTAC
42300158 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
42300180 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
42300203 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:42300206 original size:17 final size:17
Alignment explanation
Indices: 42300184--42300236 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 17
42300174 ATTACAAAAT
42300184 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
* *
42300201 CATATCATATCTACGATTG
1 CATATC-T-TCTAAGATTA
* *
42300220 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
42300237 TGTTTCCATA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 13 0.46
18 1 0.04
19 14 0.50
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:42300207 original size:22 final size:22
Alignment explanation
Indices: 42300155--42300212 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
42300145 GAAAGGTATC
*
42300155 TACAAATCAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
42300176 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
42300199 TACATATCATATCT
1 TACAAATCATATCT
42300213 ACGATTGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 19 0.58
23 11 0.33
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.34
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:42303776 original size:117 final size:118
Alignment explanation
Indices: 42303655--42303883 Score: 324
Period size: 123 Copynumber: 1.9 Consensus size: 118
42303645 TTTAAATTAT
** *
42303655 ATCTTAATACTACTTTTTACACAAATCTAATCATT-CAAAAA-A-AATGTTCAATGTTATATATT
1 ATCTTAATACTACTTTCAACACAAATCTAACCATTACAAAAATATAATGTTCAATGTTATAT-TT
42303717 -AAAATATACAAATTATTATTACAATATATAAAA-AAACCATACACTAGTCAAATCA
65 AAAAATATACAAATTATTATTACAA-A-ATAAAATAAA-CATACACTAGTCAAATCA
*
42303772 ATCTTAATATTACTTTCAACACAAATCTAACCATTCAAACAAAAATATAATGTTCAATGTTATAT
1 ATCTTAATACTACTTTCAACACAAATCTAACCATT---ACAAAAATATAATGTTCAATGTTATAT
42303837 TTAAAAATATACAAATTATTATTACAAAATAAAATAAACATACACTA
63 TTAAAAATATACAAATTATTATTACAAAATAAAATAAACATACACTA
42303884 CCAAAATTAT
Statistics
Matches: 100, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
117 31 0.31
121 21 0.21
122 7 0.07
123 41 0.41
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (118 bp):
ATCTTAATACTACTTTCAACACAAATCTAACCATTACAAAAATATAATGTTCAATGTTATATTTA
AAAATATACAAATTATTATTACAAAATAAAATAAACATACACTAGTCAAATCA
Found at i:42303928 original size:28 final size:28
Alignment explanation
Indices: 42303867--42303924 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
42303857 ATTACAAAAT
*
42303867 AAAATAAACATACACTACCAAAATTATC
1 AAAATAAACATACACTACCAAAATTAAC
**
42303895 TTAATAAACATACACTA-CAAAA-TAAC
1 AAAATAAACATACACTACCAAAATTAAC
42303921 AAAA
1 AAAA
42303925 AATATAATGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
26 5 0.20
27 5 0.20
28 15 0.60
ACGTcount: A:0.60, C:0.19, G:0.00, T:0.21
Consensus pattern (28 bp):
AAAATAAACATACACTACCAAAATTAAC
Found at i:42317129 original size:5 final size:5
Alignment explanation
Indices: 42317105--42317173 Score: 75
Period size: 5 Copynumber: 12.8 Consensus size: 5
42317095 ATAAGAATAA
* *
42317105 AAAAT AAAAA AAATAGT AAAAT AAAAAAT AATAT AATAAT AAAAT AAAAT
1 AAAAT AAAAT AAA-A-T AAAAT --AAAAT AAAAT AA-AAT AAAAT AAAAT
42317155 AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
42317174 GGGGTGACTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
5 41 0.75
6 6 0.11
7 8 0.15
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:42317131 original size:18 final size:17
Alignment explanation
Indices: 42317100--42317170 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
42317090 TAAGTATAAG
*
42317100 AATAAAAAAT-AAAAAA
1 AATATAAAATAAAAAAA
*
42317116 AATAGTAAAATAAAAAAT
1 AATA-TAAAATAAAAAAA
*
42317134 AATATAATAAT-AAAATA
1 AATATAA-AATAAAAAAA
*
42317151 AA-ATAAAATAAAATAA
1 AATATAAAATAAAAAAA
42317167 AATA
1 AATA
42317171 AAAGGGGTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
15 3 0.07
16 14 0.32
17 15 0.34
18 12 0.27
ACGTcount: A:0.77, C:0.00, G:0.01, T:0.21
Consensus pattern (17 bp):
AATATAAAATAAAAAAA
Found at i:42321628 original size:13 final size:13
Alignment explanation
Indices: 42321610--42321660 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
42321600 AGTTCTTCAT
42321610 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
42321623 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
42321636 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
42321649 TTCTTTTGAAAA
1 TGCTTTTGAAAA
42321661 ATTTAAGTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:42325038 original size:26 final size:26
Alignment explanation
Indices: 42325009--42325074 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 26
42324999 AGATAAACTC
*
42325009 ACCGGTAGAGGGCAGAGGAACAAAGA
1 ACCGGCAGAGGGCAGAGGAACAAAGA
42325035 ACCGGCAGAGGGC--A-GAACAAAGA
1 ACCGGCAGAGGGCAGAGGAACAAAGA
* *
42325058 ACTGGCAGAGGGTAGAG
1 ACCGGCAGAGGGCAGAG
42325075 ATGAGGGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 20 0.59
24 1 0.03
25 1 0.03
26 12 0.35
ACGTcount: A:0.39, C:0.17, G:0.39, T:0.05
Consensus pattern (26 bp):
ACCGGCAGAGGGCAGAGGAACAAAGA
Found at i:42327818 original size:40 final size:40
Alignment explanation
Indices: 42327753--42327833 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
42327743 ATTTACTAAA
*
42327753 GTTTTCTTATCATTCCTGTGAGGTAATAGGGACGTGTTAG
1 GTTTTCTTAGCATTCCTGTGAGGTAATAGGGACGTGTTAG
* *
42327793 GTTTTCTTAGCATTCGTGTGTGGTAATAGGGACGTGTTAG
1 GTTTTCTTAGCATTCCTGTGAGGTAATAGGGACGTGTTAG
42327833 G
1 G
42327834 CTTGAAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.19, C:0.11, G:0.31, T:0.40
Consensus pattern (40 bp):
GTTTTCTTAGCATTCCTGTGAGGTAATAGGGACGTGTTAG
Found at i:42337142 original size:27 final size:26
Alignment explanation
Indices: 42337112--42337279 Score: 228
Period size: 27 Copynumber: 6.3 Consensus size: 26
42337102 GGGTATAACA
42337112 GTCATTTTACCCTATGGGGTTATTTCG
1 GTCATTTTACCCTATGGGG-TATTTCG
*
42337139 GTCAATTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCG
*
42337166 GTTATTTTACCCTATGGGGTATTTCG
1 GTCATTTTACCCTATGGGGTATTTCG
* *
42337192 GTCATTCTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTAT-GGGGTATTTCG
*
42337219 GTCATTTTACCCTATTGAGGTATTTCG
1 GTCATTTTACCCTA-TGGGGTATTTCG
*
42337246 GTCATTTTACCCTACGGGGGTATTTCG
1 GTCATTTTACCCTA-TGGGGTATTTCG
*
42337273 GTTATTT
1 GTCATTT
42337280 ATCGACCTCT
Statistics
Matches: 125, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
26 24 0.19
27 96 0.77
28 5 0.04
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.43
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGTATTTCG
Found at i:42337241 original size:80 final size:81
Alignment explanation
Indices: 42337112--42337274 Score: 240
Period size: 80 Copynumber: 2.0 Consensus size: 81
42337102 GGGTATAACA
* * *
42337112 GTCATTTTACCCTATGGGGTTATTTCGGTCAATTTACCCTATGGGGGTATTTCGGTTATTTTACC
1 GTCATTCTACCCTATGGGGTTATTTCGGTCAATTTACCCTATGGAGGTATTTCGGTCATTTTACC
*
42337177 CTA-TGGGGTATTTCG
66 CTACGGGGGTATTTCG
* * *
42337192 GTCATTCTACCCTATAGGGG-TATTTTGGTCATTTTACCCTATTGAGGTATTTCGGTCATTTTAC
1 GTCATTCTACCCTAT-GGGGTTATTTCGGTCAATTTACCCTATGGAGGTATTTCGGTCATTTTAC
42337256 CCTACGGGGGTATTTCG
65 CCTACGGGGGTATTTCG
42337273 GT
1 GT
42337275 TATTTATCGA
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 57 0.77
81 17 0.23
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (81 bp):
GTCATTCTACCCTATGGGGTTATTTCGGTCAATTTACCCTATGGAGGTATTTCGGTCATTTTACC
CTACGGGGGTATTTCG
Found at i:42339196 original size:3 final size:3
Alignment explanation
Indices: 42339190--42339234 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
42339180 TAATTTTTGA
* * * *
42339190 TAT TAT TAT TAT TAT TAG TAT TAG TAT TAA TAT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42339235 ATATCAATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:42339319 original size:13 final size:13
Alignment explanation
Indices: 42339301--42339334 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
42339291 TAAAGTTTTT
42339301 TTATATATTATGA
1 TTATATATTATGA
*
42339314 TTATATATTATTA
1 TTATATATTATGA
42339327 TTATATAT
1 TTATATAT
42339335 CAGAACGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTATATATTATGA
Found at i:42349579 original size:50 final size:50
Alignment explanation
Indices: 42349364--42349654 Score: 205
Period size: 50 Copynumber: 5.7 Consensus size: 50
42349354 GGTAAATAGA
* * * *
42349364 TCCCATGTAAGACCATGTATGGGACATGACATAGGCATCCTTGAGATCATGAAAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGAT-AAG-AA-G
* * *
42349420 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGG-ACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAAG
* * ** * * * * * * *
42349469 TCTCATGTAAGACCATGTATCAGAAATTGCGTTGCCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAAG
* * *
42349519 TCCC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATAAGAAC
1 TCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAAG
* * ** *
42349569 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA-ATACATGAA-ACA-
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT-AAGA-AG
* * *
42349618 TCCCATGTAAGACCATGTCTCGGACATAGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
42349655 TGTTATTATC
Statistics
Matches: 190, Mismatches: 40, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
49 66 0.35
50 83 0.44
51 2 0.01
52 5 0.03
54 2 0.01
55 1 0.01
56 31 0.16
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAAG
Found at i:42352975 original size:45 final size:48
Alignment explanation
Indices: 42352891--42353010 Score: 140
Period size: 45 Copynumber: 2.5 Consensus size: 48
42352881 GAGGAGGGAT
*
42352891 CAAGGTGAAAACCTGCAAAGGGCGCTTTGAATCCT-AAAAA-GAGA-C
1 CAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCTAAAAAAGGAGAGC
* * *
42352936 TAAGGTGAAAACCCGCAAAGGGTGCTTTGAGT-CTAAAAAAAAGGGAGAGGC
1 CAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCT--AAAAAA-GGAGA-GC
42352987 CAAGGTGAAAACCCGCAAAGGGCG
1 CAAGGTGAAAACCCGCAAAGGGCG
42353011 TTCTGAGACC
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
44 2 0.03
45 28 0.45
47 5 0.08
49 4 0.06
51 23 0.37
ACGTcount: A:0.39, C:0.18, G:0.29, T:0.13
Consensus pattern (48 bp):
CAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCTAAAAAAGGAGAGC
Found at i:42354327 original size:44 final size:43
Alignment explanation
Indices: 42354273--42354472 Score: 190
Period size: 44 Copynumber: 4.6 Consensus size: 43
42354263 TAGCAGGTCT
*
42354273 TATCTCCCTGATGTTGCAGCGGAGCAGACAGAAGAAGCTAATCC
1 TATCT-CCTGAAGTTGCAGCGGAGCAGACAGAAGAAGCTAATCC
* * * * *
42354317 TATCTTCCTGAAGTTGCAGTGAAGCAGAAAAAAGAGGCTAATCC
1 TATC-TCCTGAAGTTGCAGCGGAGCAGACAGAAGAAGCTAATCC
* * * *
42354361 TATCTCCTGAAGTTGTAGCGGAGC-GA-ATTAA-AATCATAGATCT
1 TATCTCCTGAAGTTGCAGCGGAGCAGACA-GAAGAAGC-TA-ATCC
* * *
42354404 TATCTCTCTGAAGTTGCAGTGGAGCAGACAGAAAAAGATAATCC
1 TATCTC-CTGAAGTTGCAGCGGAGCAGACAGAAGAAGCTAATCC
*
42354448 TATCTCCTTGAAGTTGTAGCGGAGC
1 TATCTCC-TGAAGTTGCAGCGGAGC
42354473 GGATTAAAAT
Statistics
Matches: 126, Mismatches: 21, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
41 3 0.02
42 6 0.05
43 27 0.21
44 80 0.63
45 7 0.06
46 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (43 bp):
TATCTCCTGAAGTTGCAGCGGAGCAGACAGAAGAAGCTAATCC
Found at i:42354415 original size:87 final size:88
Alignment explanation
Indices: 42354324--42354509 Score: 288
Period size: 88 Copynumber: 2.1 Consensus size: 88
42354314 TCCTATCTTC
*
42354324 CTGAAGTTGCAGTGAAGCAGA-A-AAAAGAGGCTAATCCTATCTCC-TGAAGTTGTAGCGGAGCG
1 CTGAAGTTGCAGTGAAGCAGACAGAAAA-A-GATAATCCTATCTCCTTGAAGTTGTAGCGGAGCG
*
42354386 AATTAAAATCATAGATCTTATCTCT
64 AATTAAAATCACAGATCTTATCTCT
* *
42354411 CTGAAGTTGCAGTGGAGCAGACAGAAAAAGATAATCCTATCTCCTTGAAGTTGTAGCGGAGCGGA
1 CTGAAGTTGCAGTGAAGCAGACAGAAAAAGATAATCCTATCTCCTTGAAGTTGTAGCGGAGCGAA
42354476 TTAAAATCACAGATCTTATCTCT
66 TTAAAATCACAGATCTTATCTCT
*
42354499 CTAAAGTTGCA
1 CTGAAGTTGCA
42354510 AAGAGCAGAT
Statistics
Matches: 91, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
87 34 0.37
88 53 0.58
89 4 0.04
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (88 bp):
CTGAAGTTGCAGTGAAGCAGACAGAAAAAGATAATCCTATCTCCTTGAAGTTGTAGCGGAGCGAA
TTAAAATCACAGATCTTATCTCT
Found at i:42354506 original size:44 final size:43
Alignment explanation
Indices: 42354361--42354507 Score: 152
Period size: 44 Copynumber: 3.3 Consensus size: 43
42354351 AGGCTAATCC
*
42354361 TATCTCCTGAAGTTGTAGCGGAGCGAATTAAAATCATAGATCT
1 TATCTCCTGAAGTTGTAGCGGAGCGGATTAAAATCATAGATCT
* * * ** ** *
42354404 TATCTCTCTGAAGTTGCAGTGGAGCAGACAGAAAAAGATA-ATCC
1 TATCTC-CTGAAGTTGTAGCGGAGCGGA-TTAAAATCATAGATCT
*
42354448 TATCTCCTTGAAGTTGTAGCGGAGCGGATTAAAATCACAGATCT
1 TATCTCC-TGAAGTTGTAGCGGAGCGGATTAAAATCATAGATCT
*
42354492 TATCTCTCTAAAGTTG
1 TATCTC-CTGAAGTTG
42354508 CAAAGAGCAG
Statistics
Matches: 80, Mismatches: 19, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
43 13 0.16
44 59 0.74
45 8 0.10
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (43 bp):
TATCTCCTGAAGTTGTAGCGGAGCGGATTAAAATCATAGATCT
Found at i:42354588 original size:44 final size:45
Alignment explanation
Indices: 42354531--42354648 Score: 123
Period size: 45 Copynumber: 2.6 Consensus size: 45
42354521 GCATCTAGTT
* * * *
42354531 TTATTTCCCTAAAGTTGTAGCGGAGCAGACTGAATA-AATGAATC
1 TTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGATAACGAATC
* * * *
42354575 TTATC-CTCCTAAAGTTGCAGTGGGGCAGATTGAAGATGACGAATC
1 TTATCTC-CCTAAAGTTGCAGCGGAGCAGACTGAAGATAACGAATC
**
42354620 TTATCTCCCTAAAGTTGCAGTAGAGCAGA
1 TTATCTCCCTAAAGTTGCAGCGGAGCAGA
42354649 TTAAAGCCAA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
43 1 0.02
44 28 0.46
45 31 0.51
46 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (45 bp):
TTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGATAACGAATC
Found at i:42354590 original size:128 final size:130
Alignment explanation
Indices: 42354414--42354649 Score: 284
Period size: 128 Copynumber: 1.8 Consensus size: 130
42354404 TATCTCTCTG
* * * *
42354414 AAGTTGCAGTGGAGCAGACAGAAAAAGATAATCCTATCTCCTTGAAGTTGTAGCGGAGCGGATT-
1 AAGTTGCAGCGGAGCAGACAGAAAAAGATAATCCTATCTCCTTAAAGTTGCAGCGGAGCAGATTG
*
42354478 AAAATCAC-AGATCTTATCTCTCTAAAGTTGCA-AAGAGCAGATCGCATCTAGTTTTATTTCCCT
66 AAAATCACGA-ATCTTATCTCCCTAAAGTTGCAGAAGAGCAGATCGCATCTAGTTTTATTTCCCT
42354541 A
130 A
* * * * * *
42354542 AAGTTGTAGCGGAGCAGACTGAATAA-ATGAATCTTATCCTCC-TAAAGTTGCAGTGGGGCAGAT
1 AAGTTGCAGCGGAGCAGACAGAAAAAGAT-AATCCTAT-CTCCTTAAAGTTGCAGCGGAGCAGAT
* * *
42354605 TGAAGATGACGAATCTTATCTCCCTAAAGTTGCAGTAGAGCAGAT
64 TGAAAATCACGAATCTTATCTCCCTAAAGTTGCAGAAGAGCAGAT
42354650 TAAAGCCAAT
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
127 2 0.02
128 46 0.52
129 31 0.35
130 10 0.11
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (130 bp):
AAGTTGCAGCGGAGCAGACAGAAAAAGATAATCCTATCTCCTTAAAGTTGCAGCGGAGCAGATTG
AAAATCACGAATCTTATCTCCCTAAAGTTGCAGAAGAGCAGATCGCATCTAGTTTTATTTCCCTA
Found at i:42354713 original size:44 final size:44
Alignment explanation
Indices: 42354356--42354776 Score: 136
Period size: 44 Copynumber: 9.8 Consensus size: 44
42354346 AAAAGAGGCT
* * * *
42354356 AATCCTATCT-CCTGAAGTTGTAGC-GGAGC-GAATTAAAATCAT
1 AATCTTATCTCCCTAAAGTTGTAGCGGGAGCAG-ATTAAAATGAC
* * * * ** * *
42354398 AGATCTTATCTCTCTGAAGTTGCAG-TGGAGCAGACAGAAAAAGAT
1 A-ATCTTATCTCCCTAAAGTTGTAGCGGGAGCAGA-TTAAAATGAC
* * * * *
42354443 AATCCTATCTCCTTGAAGTTGTAGC-GGAGCGGATTAAAATCAC
1 AATCTTATCTCCCTAAAGTTGTAGCGGGAGCAGATTAAAATGAC
* * ** ***
42354486 AGATCTTATCTCTCTAAAGTTGCA--AAGAGCAGA-TCGCAT--C
1 A-ATCTTATCTCCCTAAAGTTGTAGCGGGAGCAGATTAAAATGAC
* * * *
42354526 TAGTTTTATTTCCCTAAAGTTGTAGC-GGAGCAGACTGAATAAATG--
1 -AATCTTATCTCCCTAAAGTTGTAGCGGGAGCAGA-T-TA-AAATGAC
* * *
42354571 AATCTTATC-CTCCTAAAGTTGCAGTGGG-GCAGATTGAAGATGAC
1 AATCTTATCTC-CCTAAAGTTGTAGCGGGAGCAGATT-AAAATGAC
* ** *
42354615 GAATCTTATCTCCCTAAAGTTGCAG-TAGAGCAGATT-AAA-GCC
1 -AATCTTATCTCCCTAAAGTTGTAGCGGGAGCAGATTAAAATGAC
*
42354657 AATAATTCTATCTCCCTAAAGTTGTAGCGGGA-CAGATTAAAATGAC
1 AAT--CT-TATCTCCCTAAAGTTGTAGCGGGAGCAGATTAAAATGAC
* * * * *
42354703 AGATCTTATCTCTCTGAAGTTGTA--GAGAGCAGA-TCATAT--C
1 A-ATCTTATCTCCCTAAAGTTGTAGCGGGAGCAGATTAAAATGAC
* *
42354743 TAGTCTTATCTCCCTGAAGTTGTAGC-GGAGCAGA
1 -AATCTTATCTCCCTAAAGTTGTAGCGGGAGCAGA
42354777 CTAAGCAAGT
Statistics
Matches: 282, Mismatches: 62, Indels: 71
0.68 0.15 0.17
Matches are distributed among these distances:
40 39 0.14
41 19 0.07
42 17 0.06
43 30 0.11
44 124 0.44
45 47 0.17
46 4 0.01
47 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTAAAGTTGTAGCGGGAGCAGATTAAAATGAC
Found at i:42361907 original size:17 final size:17
Alignment explanation
Indices: 42361885--42361937 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
42361875 ATAGAAAGTC
*
42361885 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAA
* *
42361902 AAAGATATAGGTATAAA
1 AAAGATATGGGTATCAA
42361919 AAAGATATGGGTATCAA
1 AAAGATATGGGTATCAA
42361936 AA
1 AA
42361938 TCTAAGATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.23
Consensus pattern (17 bp):
AAAGATATGGGTATCAA
Found at i:42368066 original size:41 final size:41
Alignment explanation
Indices: 42368021--42368139 Score: 161
Period size: 41 Copynumber: 2.9 Consensus size: 41
42368011 TCAGGTTTAT
42368021 TGCCAGTGAAACATTTCAGACTTTTAGTCTAGCAGGCTTGA
1 TGCCAGTGAAACATTTCAGACTTTTAGTCTAGCAGGCTTGA
*
42368062 TGCCAGTGAAACATTTCAGACTTTAAGTCTAGCAGGCTTGA
1 TGCCAGTGAAACATTTCAGACTTTTAGTCTAGCAGGCTTGA
* *** *
42368103 CGGTGGTGAAACATTTTAGAC-TTTATGTC-AGCAGGCT
1 TGCCAGTGAAACATTTCAGACTTTTA-GTCTAGCAGGCT
42368140 AAGTGCCAGT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
40 11 0.16
41 59 0.84
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (41 bp):
TGCCAGTGAAACATTTCAGACTTTTAGTCTAGCAGGCTTGA
Found at i:42369596 original size:17 final size:17
Alignment explanation
Indices: 42369574--42369623 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
42369564 ATAGAAAGTC
42369574 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
*
42369591 AAAGATATAGGTATCAG
1 AAAGATATGGGTATCAG
42369608 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
42369624 AAATCTGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:42375178 original size:20 final size:20
Alignment explanation
Indices: 42375153--42375191 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
42375143 AACATTCAAA
42375153 ATACCATAATCACAA-CCAAG
1 ATACCATAA-CACAAGCCAAG
42375173 ATACCATAACACAAGCCAA
1 ATACCATAACACAAGCCAA
42375192 ACCATATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.51, C:0.31, G:0.05, T:0.13
Consensus pattern (20 bp):
ATACCATAACACAAGCCAAG
Found at i:42376347 original size:25 final size:25
Alignment explanation
Indices: 42376319--42376443 Score: 142
Period size: 25 Copynumber: 5.0 Consensus size: 25
42376309 TATACTCAGT
42376319 TGAGCTATAGATTGGTATGCTCTCA
1 TGAGCTATAGATTGGTATGCTCTCA
* * * *
42376344 TGAGCTGTAAATCGGTATGCTCACA
1 TGAGCTATAGATTGGTATGCTCTCA
* *
42376369 CGAGCTATAGATTAGTATGCTCTCA
1 TGAGCTATAGATTGGTATGCTCTCA
* * * * *
42376394 TGAGTTGTAAATTGGTATGATCACA
1 TGAGCTATAGATTGGTATGCTCTCA
*
42376419 TGAGCTATAGATCGGTATGCTCTCA
1 TGAGCTATAGATTGGTATGCTCTCA
42376444 CGAGTTGTAA
Statistics
Matches: 77, Mismatches: 23, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 77 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (25 bp):
TGAGCTATAGATTGGTATGCTCTCA
Found at i:42376374 original size:50 final size:50
Alignment explanation
Indices: 42376293--42376472 Score: 234
Period size: 50 Copynumber: 3.6 Consensus size: 50
42376283 GTATGCTTAT
* * * ***
42376293 ATGAGCTGTGAATCAGTATACTCAGTTGAGCTATAGATTGGTATGCTCTC
1 ATGAGCTGTAAATCGGTATGCTCACACGAGCTATAGATTGGTATGCTCTC
*
42376343 ATGAGCTGTAAATCGGTATGCTCACACGAGCTATAGATTAGTATGCTCTC
1 ATGAGCTGTAAATCGGTATGCTCACACGAGCTATAGATTGGTATGCTCTC
* * * * *
42376393 ATGAGTTGTAAATTGGTATGATCACATGAGCTATAGATCGGTATGCTCTC
1 ATGAGCTGTAAATCGGTATGCTCACACGAGCTATAGATTGGTATGCTCTC
* *
42376443 ACGAGTTGTAAATCGGTATGCTCACACGAG
1 ATGAGCTGTAAATCGGTATGCTCACACGAG
42376473 GTGTGGGTCG
Statistics
Matches: 113, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 113 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (50 bp):
ATGAGCTGTAAATCGGTATGCTCACACGAGCTATAGATTGGTATGCTCTC
Found at i:42376457 original size:25 final size:25
Alignment explanation
Indices: 42376332--42376472 Score: 138
Period size: 25 Copynumber: 5.6 Consensus size: 25
42376322 GCTATAGATT
* *
42376332 GGTATGCTCTCATGAGCTGTAAATC
1 GGTATGCTCACACGAGCTGTAAATC
* * *
42376357 GGTATGCTCACACGAGCTATAGATT
1 GGTATGCTCACACGAGCTGTAAATC
* * * * *
42376382 AGTATGCTCTCATGAGTTGTAAATT
1 GGTATGCTCACACGAGCTGTAAATC
* * * *
42376407 GGTATGATCACATGAGCTATAGATC
1 GGTATGCTCACACGAGCTGTAAATC
* *
42376432 GGTATGCTCTCACGAGTTGTAAATC
1 GGTATGCTCACACGAGCTGTAAATC
42376457 GGTATGCTCACACGAG
1 GGTATGCTCACACGAG
42376473 GTGTGGGTCG
Statistics
Matches: 91, Mismatches: 25, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 91 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (25 bp):
GGTATGCTCACACGAGCTGTAAATC
Found at i:42376993 original size:20 final size:20
Alignment explanation
Indices: 42376965--42377002 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42376955 AACTATCATG
*
42376965 TTTTCTTTATTTTATTAACC
1 TTTTATTTATTTTATTAACC
42376985 TTTTATTTATTTTATTAA
1 TTTTATTTATTTTATTAA
42377003 TAAAATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATTTATTTTATTAACC
Found at i:42392983 original size:16 final size:16
Alignment explanation
Indices: 42392960--42392995 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
42392950 TATTATTATC
42392960 TATATTTTT-TATAGA
1 TATATTTTTATATAGA
*
42392975 TATATTTTTATCTAGA
1 TATATTTTTATATAGA
42392991 TATAT
1 TATAT
42392996 AAGATCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (16 bp):
TATATTTTTATATAGA
Found at i:42395701 original size:17 final size:17
Alignment explanation
Indices: 42395679--42395712 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42395669 ATAGACTCGC
*
42395679 TTAGATATACTTAGTAT
1 TTAGATATAATTAGTAT
42395696 TTAGATATAATTAGTAT
1 TTAGATATAATTAGTAT
42395713 AATATACGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
TTAGATATAATTAGTAT
Found at i:42401190 original size:30 final size:31
Alignment explanation
Indices: 42401150--42401209 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
42401140 TTTGGTCACT
*
42401150 TTTTGACATTTTTTCAAATTTA-CCCTTAAAG
1 TTTTGACATTTGTTC-AATTTAGCCCTTAAAG
*
42401181 TTTT-ACATTTGTTCAATTTAGTCCTTAAA
1 TTTTGACATTTGTTCAATTTAGCCCTTAAA
42401210 CCTAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 6 0.23
30 16 0.62
31 4 0.15
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (31 bp):
TTTTGACATTTGTTCAATTTAGCCCTTAAAG
Found at i:42411525 original size:24 final size:24
Alignment explanation
Indices: 42411473--42411526 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
42411463 AATAATACGT
* *
42411473 AAAGAAGTGCATGTCGTGTCAGTC
1 AAAGATGTGCATGTCGCGTCAGTC
*
42411497 AAAGATGTGCATGTCGCGTCGGTC
1 AAAGATGTGCATGTCGCGTCAGTC
*
42411521 GAAGAT
1 AAAGAT
42411527 AAGGCAACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (24 bp):
AAAGATGTGCATGTCGCGTCAGTC
Found at i:42411726 original size:15 final size:14
Alignment explanation
Indices: 42411693--42411726 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
42411683 TTTTGTTATT
*
42411693 TTTTATTTTATTCA
1 TTTTATTTTATTAA
42411707 TTTTATTATTATTAA
1 TTTTATT-TTATTAA
42411722 TTTTA
1 TTTTA
42411727 GTTGTGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATTTTATTAA
Found at i:42420325 original size:19 final size:20
Alignment explanation
Indices: 42420290--42420334 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
42420280 TTACCCTAAA
* *
42420290 CTCCCAAATATTTTTACTTT
1 CTCCCAAATACTTTTACTCT
42420310 CTCCCAAA-ACTTTTACTCT
1 CTCCCAAATACTTTTACTCT
42420329 CTCCCA
1 CTCCCA
42420335 CTTTCCCCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.40
Consensus pattern (20 bp):
CTCCCAAATACTTTTACTCT
Found at i:42422410 original size:11 final size:11
Alignment explanation
Indices: 42422394--42422428 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
42422384 TTAAACTAAG
42422394 TAAATAAATAA
1 TAAATAAATAA
42422405 TAAATAAATAA
1 TAAATAAATAA
42422416 -AAATAAA-AA
1 TAAATAAATAA
42422425 TAAA
1 TAAA
42422429 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.09
10 10 0.43
11 11 0.48
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:42423828 original size:23 final size:22
Alignment explanation
Indices: 42423776--42423828 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
42423766 TCCACGTCTT
*
42423776 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
42423798 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
42423821 TTTCTTTT
1 TTTCTTTT
42423829 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:42426195 original size:12 final size:12
Alignment explanation
Indices: 42426173--42426204 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
42426163 CATAAAAATT
42426173 TAAACTAAGTAAA
1 TAAA-TAAGTAAA
42426186 TAAATAAGTAAA
1 TAAATAAGTAAA
42426198 TAAATAA
1 TAAATAA
42426205 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (12 bp):
TAAATAAGTAAA
Found at i:42429473 original size:16 final size:17
Alignment explanation
Indices: 42429434--42429466 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
42429424 AAAGTTTAGG
42429434 GGGGAAATAATAAGTTTT
1 GGGG-AATAATAAGTTTT
42429452 GGGGAATAA-AAGTTT
1 GGGGAATAATAAGTTT
42429467 GAGGGAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (17 bp):
GGGGAATAATAAGTTTT
Found at i:42429852 original size:9 final size:9
Alignment explanation
Indices: 42429838--42429874 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42429828 TATAGTTTGA
42429838 TATTCGAAT
1 TATTCGAAT
42429847 TATTCGAAT
1 TATTCGAAT
*
42429856 TATTCGAGT
1 TATTCGAAT
42429865 TATTCGAAT
1 TATTCGAAT
42429874 T
1 T
42429875 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:42435862 original size:33 final size:33
Alignment explanation
Indices: 42435825--42435889 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
42435815 TAATACTACC
42435825 TTAGTTGACACATTATTCAAAATATAACAAATT
1 TTAGTTGACACATTATTCAAAATATAACAAATT
*
42435858 TTAGTTGGCACATTATTCAAAATATAACAAAT
1 TTAGTTGACACATTATTCAAAATATAACAAAT
42435890 AGTTTGTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (33 bp):
TTAGTTGACACATTATTCAAAATATAACAAATT
Found at i:42439455 original size:20 final size:19
Alignment explanation
Indices: 42439416--42439452 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
42439406 AAAAAAAAAG
*
42439416 AAAATATAAAATTTATATA
1 AAAAAATAAAATTTATATA
42439435 AAAAAAT-AAATTTATATA
1 AAAAAATAAAATTTATATA
42439453 TAATACATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAAATAAAATTTATATA
Found at i:42439543 original size:56 final size:55
Alignment explanation
Indices: 42439483--42439659 Score: 159
Period size: 56 Copynumber: 3.1 Consensus size: 55
42439473 AGAAAAATAC
42439483 ATATATAGAAATTATAAAATATGTATGGAAAGTATAATATGTATATACGTACATAT
1 ATATATAGAAATTATAAAATATGTATGGAAAGTATAATAT-TATATACGTACATAT
* * * * *
42439539 ATATAT--AAGTTAATAAATATATATATAGATCATAAAG-ATAATGATTACATA--TATATAT
1 ATATATAGAAATT-ATAAA-ATATGTAT-G----GAAAGTATAAT-ATTATATACGTACATAT
*
42439597 ATATATAGAAAAATTATAAAATATGTATAGAAAGTATAATA-TATATACGTACATAT
1 ATATATAG--AAATTATAAAATATGTATGGAAAGTATAATATTATATACGTACATAT
42439653 ATATATA
1 ATATATA
42439660 AATTAATAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
54 9 0.09
55 10 0.11
56 31 0.33
57 1 0.01
58 12 0.13
60 17 0.18
61 11 0.12
62 4 0.04
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.36
Consensus pattern (55 bp):
ATATATAGAAATTATAAAATATGTATGGAAAGTATAATATTATATACGTACATAT
Found at i:42439642 original size:22 final size:23
Alignment explanation
Indices: 42439591--42439643 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
42439581 GATTACATAT
*
42439591 ATATATATATATAGAAAAATTATA
1 ATATATATATATAG-AAAAGTATA
*
42439615 A-A-ATATGTATAG-AAAGTATA
1 ATATATATATATAGAAAAGTATA
42439635 ATATATATA
1 ATATATATA
42439644 CGTACATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 13 0.54
23 1 0.04
24 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.36
Consensus pattern (23 bp):
ATATATATATATAGAAAAGTATA
Found at i:42439694 original size:110 final size:112
Alignment explanation
Indices: 42439483--42439703 Score: 351
Period size: 114 Copynumber: 2.0 Consensus size: 112
42439473 AGAAAAATAC
* *
42439483 ATATATAGAAATTATAAAATATGTATGGAAAGTATAATATGTATATACGTACATATATATATAAG
1 ATATATAGAAATTATAAAATATGTATAGAAAGTATAATA-GTATATACGTACATATATATATAAA
*
42439548 TTAATAAATATATATATAGATCATAAAGATAATGATTACATATATATAT
65 TTAAT-AATATATATATAGATCAGAAAGATAATGATTACATATATATAT
42439597 ATATATAGAAAAATTATAAAATATGTATAGAAAGTATAATA-TATATACGTACATATATATATAA
1 ATATATAG--AAATTATAAAATATGTATAGAAAGTATAATAGTATATACGTACATATATATATAA
42439661 ATTAAT-A-A-ATATATAGATCAGAAAGATAATGATTACATATATA
64 ATTAATAATATATATATAGATCAGAAAGATAATGATTACATATATA
42439704 AACTTAAAAA
Statistics
Matches: 102, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
110 34 0.33
111 1 0.01
112 1 0.01
114 36 0.35
116 30 0.29
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (112 bp):
ATATATAGAAATTATAAAATATGTATAGAAAGTATAATAGTATATACGTACATATATATATAAAT
TAATAATATATATATAGATCAGAAAGATAATGATTACATATATATAT
Found at i:42440489 original size:12 final size:12
Alignment explanation
Indices: 42440459--42440489 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
42440449 ACAAAATAAA
42440459 AAAAAAAGAAAT
1 AAAAAAAGAAAT
*
42440471 AACAAAAGAAAT
1 AAAAAAAGAAAT
42440483 AAAAAAA
1 AAAAAAA
42440490 AACAACCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.84, C:0.03, G:0.06, T:0.06
Consensus pattern (12 bp):
AAAAAAAGAAAT
Found at i:42440783 original size:15 final size:15
Alignment explanation
Indices: 42440763--42440793 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42440753 AGGGTTTCTG
42440763 ACTGTAATTTGGGCC
1 ACTGTAATTTGGGCC
*
42440778 ACTGTAGTTTGGGCC
1 ACTGTAATTTGGGCC
42440793 A
1 A
42440794 TTGTTATTGT
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:0.19, C:0.19, G:0.29, T:0.32
Consensus pattern (15 bp):
ACTGTAATTTGGGCC
Found at i:42448342 original size:3 final size:3
Alignment explanation
Indices: 42448334--42448369 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
42448324 CTTATAGGCT
42448334 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
42448370 TTGAACGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:42451574 original size:11 final size:11
Alignment explanation
Indices: 42451558--42451601 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
42451548 GGTATTTTAT
42451558 AAAAATAATAC
1 AAAAATAATAC
* *
42451569 AAAAATAAAAAT
1 AAAAAT-AATAC
42451581 AAAAATAATAC
1 AAAAATAATAC
*
42451592 CAAAATAATA
1 AAAAATAATA
42451602 TAATTTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAATAATAC
Found at i:42451582 original size:23 final size:23
Alignment explanation
Indices: 42451556--42451599 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
42451546 AGGGTATTTT
42451556 ATAAAAATAATACAAAAATAAAA
1 ATAAAAATAATACAAAAATAAAA
*
42451579 ATAAAAATAATACCAAAATAA
1 ATAAAAATAATACAAAAATAA
42451600 TATAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (23 bp):
ATAAAAATAATACAAAAATAAAA
Found at i:42452289 original size:156 final size:153
Alignment explanation
Indices: 42451845--42452505 Score: 827
Period size: 159 Copynumber: 4.3 Consensus size: 153
42451835 TTAGTGTGTG
* **
42451845 TTTTATTGAAAGTAATAAAATTCGAAAAAAAAATACGAACAAAGGGCCGAAATAAGAG-TTTTTT
1 TTTTATTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAG-GTTTTTTT
* * * *
42451909 T-AATTTATTTAAAACACACACTAAATGAATACATTTCAAATATAATGTACTGAAATAATGTAAA
65 TAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGT-AA
*
42451973 ATAATAAAATTAGAAAATAGTATAT
129 ATAATAAAATTAGAAAATAATATAT
* ** * *
42451998 TTTT-TT-AAAGTAATAAACTTTGGGGAAAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTTT
1 TTTTATTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAA-GGTTTTTTT
* * * *
42452061 AAAAAATTATTTAAAAAACACAGTAAATTAATACATTTTAAACATAATGTACTAAAATAATGTAA
65 -TAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGT-A
*
42452126 AATAATAAAA-TACGAAACTAATATAT
128 AATAATAAAATTA-GAAAATAATATAT
* *
42452152 TTTTATTGAAAGTAATAAAATCCAGGAAAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTTT
1 TTTTATTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAG-G--TTTTT
*
42452217 TTTAAATTTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATTGTACTAAAATAATG
63 TTTAAA-TTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAA-TGTACTAAAATAATG
42452282 TAAAATAATAAAA-TATGAAAATAATATAT
126 T-AAATAATAAAATTA-GAAAATAATATAT
* ** * * *
42452311 ATTTATTGAAAGTAATAAAATCCGGGATTAGAATACGAACAAATGGCTGAAATAATGGTTTTTTT
1 TTTTATTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAA-GGTTTTTTT
*
42452376 TAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAGTGTAAA
65 TAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGT-AA
* *
42452441 ATAAAAAAATTAGAAAATAGTATA-
129 ATAATAAAATTAGAAAATAATATAT
* * *
42452465 TTTT-TTAAAAGTAATAAAAT-CTGAAAAAAAATACGAACAAA
1 TTTTATTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAA
42452506 AGGTCAAAAT
Statistics
Matches: 447, Mismatches: 47, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
151 42 0.09
152 25 0.06
153 21 0.05
154 83 0.19
155 40 0.09
156 84 0.19
157 14 0.03
158 47 0.11
159 90 0.20
160 1 0.00
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (153 bp):
TTTTATTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTT
AAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAT
AATAAAATTAGAAAATAATATAT
Found at i:42452661 original size:10 final size:10
Alignment explanation
Indices: 42452635--42452677 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
42452625 AAAATATTTA
*
42452635 TATTGTTTTG
1 TATTTTTTTG
42452645 ATATTTTTTT-
1 -TATTTTTTTG
42452655 TATTTTTTTG
1 TATTTTTTTG
42452665 TATTATTTTTG
1 TATT-TTTTTG
42452676 TA
1 TA
42452678 AAGGACCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 9 0.31
10 4 0.14
11 16 0.55
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (10 bp):
TATTTTTTTG
Found at i:42452663 original size:20 final size:20
Alignment explanation
Indices: 42452635--42452674 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42452625 AAAATATTTA
42452635 TATTGTTTTGATATT-TTTTT
1 TATTGTTTTG-TATTATTTTT
*
42452655 TATTTTTTTGTATTATTTTT
1 TATTGTTTTGTATTATTTTT
42452675 GTAAAGGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (20 bp):
TATTGTTTTGTATTATTTTT
Found at i:42454161 original size:123 final size:124
Alignment explanation
Indices: 42453942--42454220 Score: 499
Period size: 123 Copynumber: 2.3 Consensus size: 124
42453932 TTATTTCTAG
*
42453942 TTGACGTTTCT-GGTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTAT
1 TTGACGTTTCTAAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTAT
* *
42454006 GAAATTGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAA-TTTTT
65 GAAATCGTGCCATCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
*
42454065 TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTATG
42454130 AAATCGTGCCATCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
66 AAATCGTGCCATCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
42454189 TTGACGTTTCTAAGCAAATAGTATAAAATCGC
1 TTGACGTTTCTAAGCAAATAGTATAAAATCGC
42454221 GCCCTCGTGG
Statistics
Matches: 150, Mismatches: 4, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
123 112 0.75
124 38 0.25
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTATG
AAATCGTGCCATCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
Found at i:42457420 original size:23 final size:25
Alignment explanation
Indices: 42457363--42457460 Score: 88
Period size: 29 Copynumber: 3.4 Consensus size: 25
42457353 TTTTGTTAAT
42457363 GGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTTTTAATTAAATTA-G--A
42457391 GGGTTAGGGTTTTTAATTAAATTAAGTTA
1 -GGTTAGGGTTTTTAATTAAATT-AG--A
42457420 GGGTTTAGGGTTTTTAATTAAATTAGATTA
1 -GG-TTAGGGTTTTTAATTAAATTAG---A
42457450 GGTTAGGGTTT
1 GGTTAGGGTTT
42457461 AAGGTTTTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.14
29 33 0.50
30 24 0.36
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.46
Consensus pattern (25 bp):
GGTTAGGGTTTTTAATTAAATTAGA
Found at i:42457430 original size:30 final size:30
Alignment explanation
Indices: 42457365--42458167 Score: 1049
Period size: 30 Copynumber: 26.8 Consensus size: 30
42457355 TTGTTAATGG
42457365 TTAGGGTTTTTAATTAAATTAGGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457394 TTAGGGTTTTTAATTAAATTAAGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
42457424 TTAGGGTTTTTAATTAAATTAGATTAGGTTAGGGT
1 TTAGGGTTTTTAATT--A--A-ATTAGGTTAGGGT
*
42457459 TTAAGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
42457489 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGT
1 TTAGGGTTTTTAATTAAATTAGGTTA--G----GGT
*
42457525 TTAGGGTTTTTAATTAAATTAAGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457554 GTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457584 TTAGGGTTTTTAATTAAATTAGGTTAGGAT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457614 TTAGGATTTTTAATTAAATTAGGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457643 TTAGAGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457673 TTACGGTTTTTAATTAAATTAGGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457702 TTAGGGTTTTTAATTAAATTAAGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457732 TTAGGGTTTTTAATTAAATTAAGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
42457761 TTA-GGTTTTTAATTAAATTAGGTTA--G-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
42457787 -T---GTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457813 TTAGGGTTTTTAATTAAATTAAGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
* *
42457843 TTAGGATTTTTAATTAAATTAGGTTAAGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
42457872 TTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG-T
42457903 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGT
1 ----TTAGGGTTTTTAATT-AA--A--TTA-GG-TTAGGGT
42457944 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
**
42457974 TTACAGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
* *
42458004 TTAGAGTTTTTAATTAAATTAGGTTAGAG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42458033 TTAGGGTTTTTAATTAAATTAAGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
42458062 TTAGGGTTTTTAATT-AA--A--TTA-GG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
42458085 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
** *
42458115 TTATAGTTTTTAATTAAATTAGGTTAGTGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
42458145 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
42458168 ATTTTTATTA
Statistics
Matches: 696, Mismatches: 36, Indels: 83
0.85 0.04 0.10
Matches are distributed among these distances:
23 38 0.05
24 5 0.01
25 2 0.00
26 3 0.00
27 1 0.00
28 26 0.04
29 182 0.26
30 326 0.47
31 3 0.00
32 5 0.01
33 1 0.00
34 3 0.00
35 41 0.06
36 32 0.05
37 15 0.02
38 1 0.00
40 3 0.00
41 3 0.00
42 6 0.01
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.46
Consensus pattern (30 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGT
Found at i:42457437 original size:59 final size:60
Alignment explanation
Indices: 42457365--42458167 Score: 1049
Period size: 59 Copynumber: 13.4 Consensus size: 60
42457355 TTGTTAATGG
*
42457365 TTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAAGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457424 TTAGGGTTTTTAATTAAATTAGATTAGGTTAGGGTTTAAGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATT--A--A-ATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457489 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTAGGGTTTTTAATTAAATTAAGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTA--G----GGTTTAGGGTTTTTAATTAAATTAGGTTAGGG
42457554 -
60 T
* *
42457554 GTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGAT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
* *
42457614 TTAGGATTTTTAATTAAATTAGGTTAGGG-TTAGAGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
* *
42457673 TTACGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAAGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457732 TTAGGGTTTTTAATTAAATTAAGTTAGGG-TTA-GGTTTTTAATTAAATTAGGTTA--G-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42457787 -T---GTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAAGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
* *
42457843 TTAGGATTTTTAATTAAATTAGGTTAAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGG-T
42457903 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTAGGGTTTTTAATTAAATTAGGT
1 ----TTAGGGTTTTTAATT-AA--A--TTA-GG-TTAGGGTTTAGGGTTTTTAATTAAATTAGGT
42457968 TAGGGT
55 TAGGGT
** * *
42457974 TTACAGTTTTTAATTAAATTAGGTTAGGGTTTAGAGTTTTTAATTAAATTAGGTTAGAG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
42458033 TTAGGGTTTTTAATTAAATTAAGTTAGGG-TTAGGGTTTTTAATT-AA--A--TTA-GG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
** *
42458085 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTATAGTTTTTAATTAAATTAGGTTAGTGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
42458145 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
42458168 ATTTTTATTA
Statistics
Matches: 663, Mismatches: 38, Indels: 85
0.84 0.05 0.11
Matches are distributed among these distances:
51 23 0.03
52 32 0.05
53 37 0.06
54 3 0.00
55 2 0.00
56 2 0.00
57 3 0.00
58 38 0.06
59 213 0.32
60 116 0.17
61 4 0.01
62 4 0.01
63 3 0.00
64 27 0.04
65 70 0.11
66 32 0.05
67 14 0.02
69 3 0.00
70 2 0.00
71 6 0.01
72 29 0.04
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.46
Consensus pattern (60 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
Found at i:42457568 original size:24 final size:23
Alignment explanation
Indices: 42457541--42457585 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
42457531 TTTTTAATTA
*
42457541 AATTAAGTTAGGGGTAGGGTTTTT
1 AATTAAATTA-GGGTAGGGTTTTT
*
42457565 AATTAAATTAGGTTAGGGTTT
1 AATTAAATTAGGGTAGGGTTT
42457586 AGGGTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (23 bp):
AATTAAATTAGGGTAGGGTTTTT
Found at i:42457839 original size:23 final size:23
Alignment explanation
Indices: 42457732--42457844 Score: 100
Period size: 23 Copynumber: 4.4 Consensus size: 23
42457722 AAGTTAGGGT
42457732 TTAGGGTTTTTAATTAAATTAAG
1 TTAGGGTTTTTAATTAAATTAAG
*
42457755 TTAGGGTTAGGTTTTTAATTAAATTAGG
1 TTA--G---GGTTTTTAATTAAATTAAG
*
42457783 TTAGTGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTA----A--G
42457812 TTTAGGGTTTTTAATTAAATTAAG
1 -TTAGGGTTTTTAATTAAATTAAG
42457836 TTAGGGTTT
1 TTAGGGTTT
42457845 AGGATTTTTA
Statistics
Matches: 74, Mismatches: 4, Indels: 24
0.73 0.04 0.24
Matches are distributed among these distances:
23 28 0.38
24 1 0.01
25 1 0.01
26 2 0.03
28 21 0.28
29 1 0.01
30 20 0.27
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (23 bp):
TTAGGGTTTTTAATTAAATTAAG
Found at i:42457902 original size:23 final size:23
Alignment explanation
Indices: 42457718--42457814 Score: 104
Period size: 23 Copynumber: 3.9 Consensus size: 23
42457708 TTTTTAATTA
*
42457718 AATTAAGTTAGGGTTTAGGGTTTTT
1 AATTAAATTA-GG-TTAGGGTTTTT
*
42457743 AATTAAATTAAGTTAGGGTTAGGTTTTT
1 AATTAAATTAGGTTA--G---GGTTTTT
*
42457771 AATTAAATTAGGTTAGTGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
42457794 AATTAAATTAGGTTAGGGTTT
1 AATTAAATTAGGTTAGGGTTT
42457815 AGGGTTTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
23 29 0.47
24 1 0.02
25 10 0.16
26 1 0.02
28 21 0.34
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (23 bp):
AATTAAATTAGGTTAGGGTTTTT
Found at i:42458146 original size:23 final size:23
Alignment explanation
Indices: 42458049--42458116 Score: 118
Period size: 23 Copynumber: 2.9 Consensus size: 23
42458039 TTTTTAATTA
*
42458049 AATTAAGTTAGGGTTAGGGTTTTT
1 AATTAAATTA-GGTTAGGGTTTTT
42458073 AATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
42458096 AATTAAATTAGGTTAGGGTTT
1 AATTAAATTAGGTTAGGGTTT
42458117 ATAGTTTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 34 0.79
24 9 0.21
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (23 bp):
AATTAAATTAGGTTAGGGTTTTT
Found at i:42460389 original size:25 final size:25
Alignment explanation
Indices: 42460339--42460394 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
42460329 CTTTTATAAC
*
42460339 AAATAATAAATTAATAATTATCTAA
1 AAATAATAAATTAATAAATATCTAA
*
42460364 AAATACATAAA-TAA-AAATATCT-T
1 AAATA-ATAAATTAATAAATATCTAA
42460387 AAATAATA
1 AAATAATA
42460395 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 3 0.11
23 5 0.18
24 7 0.25
25 8 0.29
26 5 0.18
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAATAAATTAATAAATATCTAA
Found at i:42460588 original size:30 final size:30
Alignment explanation
Indices: 42460552--42460610 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
42460542 TTAATATGGA
*
42460552 TTTGAGAGATTTTTGGAAGGAAATTGAGAG
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAG
42460582 TTTGAGAGAATTTTGGAAGGAAATTGAGA
1 TTTGAGAGAATTTTGGAAGGAAATTGAGA
42460611 TAGGATTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (30 bp):
TTTGAGAGAATTTTGGAAGGAAATTGAGAG
Found at i:42462005 original size:7 final size:7
Alignment explanation
Indices: 42461993--42462033 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
42461983 AGATAATTGA
42461993 CTAAACC
1 CTAAACC
*
42462000 CTAAACT
1 CTAAACC
42462007 CTAAACC
1 CTAAACC
*
42462014 CTAAACT
1 CTAAACC
*
42462021 TTAAACC
1 CTAAACC
42462028 CTAAAC
1 CTAAAC
42462034 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:42462012 original size:14 final size:14
Alignment explanation
Indices: 42461993--42462038 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
42461983 AGATAATTGA
42461993 CTAAACCCTAAACT
1 CTAAACCCTAAACT
42462007 CTAAACCCTAAACT
1 CTAAACCCTAAACT
*
42462021 TTAAACCCTAAACT
1 CTAAACCCTAAACT
42462035 -TAAA
1 CTAAA
42462039 AATTAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 4 0.13
14 27 0.87
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (14 bp):
CTAAACCCTAAACT
Found at i:42476335 original size:40 final size:39
Alignment explanation
Indices: 42476260--42476359 Score: 100
Period size: 40 Copynumber: 2.6 Consensus size: 39
42476250 ATAATGAAAT
*
42476260 ATTTTTAGGTATTTTTAGAATTTGTTTTCAAATTTTTTGG
1 ATTTTTAGGTATTTTTAGAATTTCTTTT-AAATTTTTTGG
* *
42476300 ATTTTTTGGTATTTTTAGAAATTTCTCTTT-GATTTTTT--
1 ATTTTTAGGTATTTTTAG-AATTTCT-TTTAAATTTTTTGG
* *
42476338 ATTTTTA-TTAATTTTAGAATTT
1 ATTTTTAGGTATTTTTAGAATTT
42476360 TTAAAATACG
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
36 5 0.10
37 8 0.15
38 6 0.12
40 24 0.46
41 6 0.12
42 3 0.06
ACGTcount: A:0.23, C:0.03, G:0.11, T:0.63
Consensus pattern (39 bp):
ATTTTTAGGTATTTTTAGAATTTCTTTTAAATTTTTTGG
Found at i:42479135 original size:33 final size:34
Alignment explanation
Indices: 42479080--42479157 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
42479070 GACTCACTCA
* ** *
42479080 TGTTTATTGTCTCGGTGGACTTA-CTTTGCTCTG
1 TGTTTATTGTCTCGATAAACTTATCTTTGCTCCG
* *
42479113 TGTTTACTGTCTCGATAAACTTATCTTTGTTCCG
1 TGTTTATTGTCTCGATAAACTTATCTTTGCTCCG
42479147 TGTTTATTGTC
1 TGTTTATTGTC
42479158 CCAACAGACT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 19 0.51
34 18 0.49
ACGTcount: A:0.13, C:0.18, G:0.19, T:0.50
Consensus pattern (34 bp):
TGTTTATTGTCTCGATAAACTTATCTTTGCTCCG
Found at i:42479150 original size:34 final size:34
Alignment explanation
Indices: 42479080--42479191 Score: 109
Period size: 34 Copynumber: 3.3 Consensus size: 34
42479070 GACTCACTCA
* * * * *
42479080 TGTTTATTGTCTCGGTGGACTTA-CTTTGCTCTG
1 TGTTTACTGTCTCGATAGACTTATCTTTGTTCCG
*
42479113 TGTTTACTGTCTCGATAAACTTATCTTTGTTCCG
1 TGTTTACTGTCTCGATAGACTTATCTTTGTTCCG
* * * * * *
42479147 TGTTTATTGTCCCAACAGACTTATCCTTCTTCCG
1 TGTTTACTGTCTCGATAGACTTATCTTTGTTCCG
42479181 TGTTTACTGTC
1 TGTTTACTGTC
42479192 CCAACAGGCT
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
33 19 0.30
34 45 0.70
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (34 bp):
TGTTTACTGTCTCGATAGACTTATCTTTGTTCCG
Found at i:42479192 original size:34 final size:34
Alignment explanation
Indices: 42479112--42479205 Score: 116
Period size: 34 Copynumber: 2.8 Consensus size: 34
42479102 ACTTTGCTCT
* * * * * *
42479112 GTGTTTACTGTCTCGATAAACTTATCTTTGTTCC
1 GTGTTTACTGTCCCAACAGACTTATCCTTCTTCC
*
42479146 GTGTTTATTGTCCCAACAGACTTATCCTTCTTCC
1 GTGTTTACTGTCCCAACAGACTTATCCTTCTTCC
*
42479180 GTGTTTACTGTCCCAACAGGCTTATC
1 GTGTTTACTGTCCCAACAGACTTATC
42479206 TATGTGGATG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (34 bp):
GTGTTTACTGTCCCAACAGACTTATCCTTCTTCC
Found at i:42479412 original size:51 final size:49
Alignment explanation
Indices: 42479331--42479427 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 49
42479321 TATCATAACA
* * *
42479331 TCTTTCATTTATGGTCTTACACTGATTACCTTATACCTTGCTACCATGGCG
1 TCTTTCATTCATGGTCTTACACTCATTACCTT-TACCGTG-TACCATGGCG
*
42479382 TCTTTCATTCATGGTCTTATAC-CATATACCTTTACCGTGTACCATG
1 TCTTTCATTCATGGTCTTACACTCAT-TACCTTTACCGTGTACCATG
42479428 TTGCCATGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 7 0.17
50 8 0.20
51 26 0.63
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (49 bp):
TCTTTCATTCATGGTCTTACACTCATTACCTTTACCGTGTACCATGGCG
Found at i:42488090 original size:25 final size:25
Alignment explanation
Indices: 42488062--42488113 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
42488052 ACTATTGATC
42488062 AAACATTGTATATTATTTGAATATT
1 AAACATTGTATATTATTTGAATATT
42488087 AAACATTGTATATTATTTGAATATT
1 AAACATTGTATATTATTTGAATATT
42488112 AA
1 AA
42488114 TATAAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (25 bp):
AAACATTGTATATTATTTGAATATT
Found at i:42502919 original size:50 final size:49
Alignment explanation
Indices: 42502853--42503041 Score: 193
Period size: 50 Copynumber: 3.8 Consensus size: 49
42502843 AACGAAACAG
* * * * *
42502853 AATAATATATAGAACAATTTGAAGTAAATAATATAAAACAATCTAAAGTA
1 AATAATATATAAAACAATTTAAAATAAATAATATAAAACGAT-TAAAATA
* *
42502903 AATAATATGTAAAACAAATTAAAATAAATAATATACAAAGCGATTTAAAATA
1 AATAATATATAAAACAATTTAAAATAAATAATATA-AAA-CGA-TTAAAATA
* * * *
42502955 AATAACATATAAGACAATTTAAAAT-AAT-ATATAAAAGGCTTAAAATA
1 AATAATATATAAAACAATTTAAAATAAATAATATAAAACGATTAAAATA
* *
42503002 AATAATATGTAAAAAGAAGTTTAAAATAAATAATATAAAA
1 AATAATATAT-AAAACAA-TTTAAAATAAATAATATAAAA
42503042 ATTAGTTTTT
Statistics
Matches: 115, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
47 16 0.14
48 6 0.05
49 11 0.10
50 38 0.33
51 14 0.12
52 29 0.25
53 1 0.01
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.28
Consensus pattern (49 bp):
AATAATATATAAAACAATTTAAAATAAATAATATAAAACGATTAAAATA
Found at i:42502978 original size:26 final size:26
Alignment explanation
Indices: 42502853--42503267 Score: 166
Period size: 26 Copynumber: 15.8 Consensus size: 26
42502843 AACGAAACAG
* * *
42502853 AATAATATATAGAACAATTTGAAGTA
1 AATAATATATAAAACAATTTAAAATA
* *
42502879 AAT-A-ATATAAAACAATCTAAAGTA
1 AATAATATATAAAACAATTTAAAATA
* *
42502903 AATAATATGTAAAACAAATTAAAATA
1 AATAATATATAAAACAATTTAAAATA
* * *
42502929 AATAATATACAAAGCGATTTAAAATA
1 AATAATATATAAAACAATTTAAAATA
* *
42502955 AATAACATATAAGACAATTTAAAAT-
1 AATAATATATAAAACAATTTAAAATA
*
42502980 AAT-ATATA-AAAGGC---TTAAAATA
1 AATAATATATAAA-ACAATTTAAAATA
* *
42503002 AATAATATGTAAAAAGAAGTTTAAAATA
1 AATAATATAT-AAAACAA-TTTAAAATA
* *
42503030 AATAATATA-AAAATTAGTTTTTAAAAAATA
1 AATAATATATAAAA-CA--ATTT--AAAATA
* * **
42503060 ACTGATATATATAAAAAGACAGTACAAAATA
1 A---ATA-ATATATAAA-ACAATTTAAAATA
*
42503091 AATAAATAATATATATGACAATTTAAAAATA
1 AAT-AAT-ATATA-A-AACAATTT-AAAATA
*
42503122 AATAATATATAAAA-AATTTAAAATG
1 AATAATATATAAAACAATTTAAAATA
* * * ** *
42503147 GATAATAGTTTGAAGTAGTTTAAAAT-
1 AATAATA-TATAAAACAATTTAAAATA
* * **
42503173 -A-CATGT-GGAAA-AA-TTAAAATA
1 AATAATATATAAAACAATTTAAAATA
*
42503194 AATAATA-ATAAAACAATATAAAATA
1 AATAATATATAAAACAATTTAAAATA
*
42503219 AATAATATATGAGAAAAAAGGTTTAAAATA
1 AATAATATAT-A-AAACAA--TTTAAAATA
42503249 AATAA-ATA-AATAACAATTT
1 AATAATATATAA-AACAATTT
42503268 TGCGAAAATA
Statistics
Matches: 293, Mismatches: 55, Indels: 83
0.68 0.13 0.19
Matches are distributed among these distances:
20 7 0.02
21 8 0.03
22 7 0.02
23 12 0.04
24 29 0.10
25 37 0.13
26 76 0.26
27 17 0.06
28 29 0.10
29 13 0.04
30 28 0.10
31 16 0.05
33 4 0.01
34 5 0.02
35 4 0.01
36 1 0.00
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (26 bp):
AATAATATATAAAACAATTTAAAATA
Found at i:42503131 original size:60 final size:58
Alignment explanation
Indices: 42502996--42503136 Score: 142
Period size: 60 Copynumber: 2.4 Consensus size: 58
42502986 TAAAAGGCTT
* ** * ***
42502996 AAAATAAATAATATGTAAAAAGAAGTTTAAAATAAATAATATAAAAATTAGTTTTTAA
1 AAAATAAATAATATATAAAAAGAAGTACAAAATAAATAATATAAAAATGACAATTTAA
*
42503054 AAAATAACTGATATATATAAAAAGACAGTACAAAATAAATAA-ATAATATATATGACAATTT-A
1 AAAATAAAT-A-ATATATAAAAAGA-AGTACAAAATAAATAATATAA-A-A-ATGACAATTTAA
42503116 AAAATAAATAATATATAAAAA
1 AAAATAAATAATATATAAAAA
42503137 ATTTAAAATG
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
58 8 0.12
59 1 0.01
60 27 0.40
61 16 0.24
62 10 0.15
63 6 0.09
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (58 bp):
AAAATAAATAATATATAAAAAGAAGTACAAAATAAATAATATAAAAATGACAATTTAA
Found at i:42503144 original size:25 final size:25
Alignment explanation
Indices: 42503090--42503253 Score: 79
Period size: 27 Copynumber: 6.4 Consensus size: 25
42503080 AGTACAAAAT
* *
42503090 AAATAAATAATATATATGACAATTTAA
1 AAATAAATAATATATA-AAAAATTT-A
42503117 AAATAAATAATATATAAAAAATTTA
1 AAATAAATAATATATAAAAAATTTA
** * ** *
42503142 AAATGGATAATAGTTTGAAGTAGTTTA
1 AAATAAATAATA-TAT-AAAAAATTTA
* * **
42503169 AAAT--A-CATGT-GGAAAAA-TTA
1 AAATAAATAATATATAAAAAATTTA
*
42503189 AAATAAATAATA-ATAAAACAATATA
1 AAATAAATAATATATAAAA-AATTTA
42503214 AAATAAATAATATATGAGAAAAAAGGTTTA
1 AAATAAATAATATAT---AAAAAA--TTTA
42503244 AAATAAATAA
1 AAATAAATAA
42503254 ATAAATAACA
Statistics
Matches: 102, Mismatches: 21, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
20 7 0.07
21 2 0.02
22 1 0.01
23 6 0.06
24 4 0.04
25 26 0.25
26 10 0.10
27 27 0.26
28 2 0.02
29 4 0.04
30 13 0.13
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (25 bp):
AAATAAATAATATATAAAAAATTTA
Found at i:42503225 original size:14 final size:16
Alignment explanation
Indices: 42503187--42503227 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
42503177 GTGGAAAAAT
42503187 TAAAATAA-ATAATAA
1 TAAAATAATATAATAA
*
42503202 TAAAACAATATAA-AA
1 TAAAATAATATAATAA
42503217 T-AAATAATATA
1 TAAAATAATATA
42503228 TGAGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 10 0.43
16 4 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAATAATATAATAA
Found at i:42504083 original size:19 final size:21
Alignment explanation
Indices: 42504059--42504104 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
42504049 ATAAACTACC
42504059 TTTGAAATCT-CT-ATTTTTG
1 TTTGAAATCTACTGATTTTTG
*
42504078 TTTGAAATTTACTGATTTTTG
1 TTTGAAATCTACTGATTTTTG
42504099 TATTGA
1 T-TTGA
42504105 TTCTCTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
21 8 0.35
22 4 0.17
ACGTcount: A:0.24, C:0.07, G:0.13, T:0.57
Consensus pattern (21 bp):
TTTGAAATCTACTGATTTTTG
Found at i:42522990 original size:16 final size:16
Alignment explanation
Indices: 42522969--42523014 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
42522959 TTTATATAAT
42522969 TTAAATTCAGTACTTA
1 TTAAATTCAGTACTTA
*
42522985 TTAAATTCAATA-TTA
1 TTAAATTCAGTACTTA
*
42523000 -AAAATTCAGTACTTA
1 TTAAATTCAGTACTTA
42523015 ATTTCTTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 9 0.35
15 6 0.23
16 11 0.42
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.41
Consensus pattern (16 bp):
TTAAATTCAGTACTTA
Found at i:42528561 original size:5 final size:5
Alignment explanation
Indices: 42528551--42528578 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
42528541 CTGACCTTAA
42528551 TCTAG TCTAG TCTAG TCTAG TCTAG TCT
1 TCTAG TCTAG TCTAG TCTAG TCTAG TCT
42528579 CCTTTGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (5 bp):
TCTAG
Found at i:42528831 original size:15 final size:16
Alignment explanation
Indices: 42528811--42528845 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42528801 TTTTTTTAAT
42528811 TTCTAAGT-AAGGAAA
1 TTCTAAGTAAAGGAAA
*
42528826 TTCTAAGTAAAGGAAT
1 TTCTAAGTAAAGGAAA
42528842 TTCT
1 TTCT
42528846 TTTTGTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (16 bp):
TTCTAAGTAAAGGAAA
Found at i:42536989 original size:18 final size:18
Alignment explanation
Indices: 42536966--42537008 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
42536956 TATACGTATG
42536966 TTATTTACATTAT-TATTA
1 TTATTTACATTATATA-TA
* *
42536984 TTATTTTCTTTATATATA
1 TTATTTACATTATATATA
42537002 TTATTTA
1 TTATTTA
42537009 TCTAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTACATTATATATA
Found at i:42548266 original size:15 final size:14
Alignment explanation
Indices: 42548243--42548275 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
42548233 TTGATTCCTA
42548243 AAAAAATGA--ATG
1 AAAAAATGATGATG
42548255 AAAAAATGATGATG
1 AAAAAATGATGATG
42548269 AAAAAAT
1 AAAAAAT
42548276 AAAAATAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
14 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (14 bp):
AAAAAATGATGATG
Found at i:42549621 original size:44 final size:44
Alignment explanation
Indices: 42549570--42549930 Score: 194
Period size: 44 Copynumber: 7.8 Consensus size: 44
42549560 AAGCCAGAAT
* *
42549570 TCTTATCTCCCTGAGATTATAGCGTAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
* * * * **
42549614 TCCTATCTCCCTAAGGTTACAGTGGAGCAGATT-AAAATAAAG-AA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT--AGTAA
* * * *
42549658 TCTTATCTCTCTGA-AGTTACAACAGAGTAGATCGCATCAGATTGAAGCCAGAAA
1 TCTTATCTCCCTGAGA-TT---ACAGCG--GA--G---CAGATTGAAGCTAGTAA
*
42549712 TCTTATCACCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
* * ** ** *
42549756 TCCTATCTCCCTGAGATTACAGTGGAGTGGATT-AAAATAAAG-GA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT--AGTAA
* * * *
42549800 TCTTATCTCTCTGA-AGTTACTGCATAGTAGATCGCATCAGATTGAAGCCAGAAA
1 TCTTATCTCCCTGAGA-TTACAGC---G--GA--G---CAGATTGAAGCTAGTAA
*
42549854 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCAAGTAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
* * *
42549898 TCCTATCTCCCTGAGATTACAGTGGAGCGGATT
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATT
42549931 AAGATAAAGG
Statistics
Matches: 239, Mismatches: 46, Indels: 64
0.68 0.13 0.18
Matches are distributed among these distances:
43 7 0.03
44 148 0.62
45 4 0.02
47 8 0.03
49 8 0.03
51 8 0.03
53 4 0.02
54 46 0.19
55 6 0.03
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
Found at i:42549815 original size:142 final size:142
Alignment explanation
Indices: 42549559--42549981 Score: 702
Period size: 142 Copynumber: 3.0 Consensus size: 142
42549549 GGAACAAATC
* * *
42549559 GAAGCCAGAATTCTTATCTCCCTGAGATTATAGCGTAGCAGATTGAAGCTAGTAATCCTATCTCC
1 GAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCC
* * * * *
42549624 CTAAGGTTACAGTGGAGCAGATTAAAATAAAGAATCTTATCTCTCTGAAGTTACAACAGAGTAGA
66 CTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGA
42549689 TCGCATCAGATT
131 TCGCATCAGATT
*
42549701 GAAGCCAGAAATCTTATCACCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCC
1 GAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCC
* * *
42549766 CTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACTGCATAGTAGA
66 CTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGA
42549831 TCGCATCAGATT
131 TCGCATCAGATT
*
42549843 GAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCAAGTAATCCTATCTCC
1 GAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCC
* *
42549908 CTGAGATTACAGTGGAGCGGATTAAGATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGA
66 CTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGA
*
42549973 TCGTATCAG
131 TCGCATCAG
42549982 GTCTTATCTC
Statistics
Matches: 261, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
142 261 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (142 bp):
GAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCC
CTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGA
TCGCATCAGATT
Found at i:42549949 original size:44 final size:44
Alignment explanation
Indices: 42549837--42549973 Score: 127
Period size: 44 Copynumber: 3.1 Consensus size: 44
42549827 TAGATCGCAT
** * *
42549837 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGAAAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* *
42549881 CAGATTGAAGCAAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGAAAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * * *
42549925 CGGATT-AAGATAAAG-GATCTTATCTCTCTGA-AGTTACAGTAGAG
1 CAGATTGAAG--AAAGTAATCTTATCTCCCTGAGA-TTACAGTGGAG
*
42549969 TAGAT
1 CAGAT
42549974 CGTATCAGGT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
43 4 0.05
44 71 0.91
45 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (44 bp):
CAGATTGAAGAAAGTAATCTTATCTCCCTGAGATTACAGTGGAG
Found at i:42556258 original size:67 final size:67
Alignment explanation
Indices: 42556179--42556314 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
42556169 CTGTCATACG
*
42556179 TAGAAGTGTTGGTGCTGAAAAAACAATAGACTTGTTGAAATTTATGGACTGGCTCGAGCACTGCT
1 TAGAAGTGTTGGTGCTGAAAAAACAATAGACTTGTTGAAATTTATGGACTGACTCGAGCACTGCT
42556244 CA
66 CA
42556246 TAGAAGTGTTGGTGCTGAAAAAACAATAGACTTGTTGAAATTTATGGACTGACTCGAGCACTGCT
1 TAGAAGTGTTGGTGCTGAAAAAACAATAGACTTGTTGAAATTTATGGACTGACTCGAGCACTGCT
42556311 CA
66 CA
42556313 TA
1 TA
42556315 CTCTCACAAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (67 bp):
TAGAAGTGTTGGTGCTGAAAAAACAATAGACTTGTTGAAATTTATGGACTGACTCGAGCACTGCT
CA
Found at i:42557236 original size:30 final size:31
Alignment explanation
Indices: 42557171--42557242 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
42557161 ACAATTGAAT
*
42557171 CAAAATCAAAGTTTTATGTGTATATTTCAAC
1 CAAAATCAAAGTTTTATGTGTATATTGCAAC
42557202 CAAAATCAAA-TTTTAATGTGTATAGTTGC-A-
1 CAAAATCAAAGTTTT-ATGTGTATA-TTGCAAC
42557232 CAAAATCAAAG
1 CAAAATCAAAG
42557243 ATTATGTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 14 0.38
31 20 0.54
32 3 0.08
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.33
Consensus pattern (31 bp):
CAAAATCAAAGTTTTATGTGTATATTGCAAC
Found at i:42557920 original size:2 final size:2
Alignment explanation
Indices: 42557913--42557942 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42557903 CTGAATTGAG
42557913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42557943 CCGAGGCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42558936 original size:18 final size:18
Alignment explanation
Indices: 42558913--42558958 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
42558903 TAATTGGATG
*
42558913 CTTAAATATGTTTTAAAA
1 CTTAAATATGTTGTAAAA
*
42558931 CTTAAATATGTTGTAACA
1 CTTAAATATGTTGTAAAA
*
42558949 CATAAATATG
1 CTTAAATATG
42558959 GGGTGGTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (18 bp):
CTTAAATATGTTGTAAAA
Found at i:42559524 original size:9 final size:9
Alignment explanation
Indices: 42559510--42559547 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
42559500 TGACCAGCCA
42559510 AAAAATATT
1 AAAAATATT
42559519 AAAAATA-T
1 AAAAATATT
*
42559527 AAAAGTTATT
1 AAAA-ATATT
42559537 AAAAATATT
1 AAAAATATT
42559546 AA
1 AA
42559548 GATTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 5 0.20
9 15 0.60
10 5 0.20
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAAATATT
Found at i:42559930 original size:30 final size:29
Alignment explanation
Indices: 42559865--42559939 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
42559855 ATGAATGAAA
*
42559865 TTTTTAACAAAAATG-ATTAATTTGCTCTT
1 TTTTTAACAAAAA-GAATTAATTTGATCTT
42559894 TGTTTTAACAAACAAGAATTAATTT-ATCTAT
1 T-TTTTAACAAA-AAGAATTAATTTGATCT-T
*
42559925 TTTTTAATAAAAAGA
1 TTTTTAACAAAAAGA
42559940 TAAAATGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 5 0.12
30 23 0.57
31 12 0.30
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (29 bp):
TTTTTAACAAAAAGAATTAATTTGATCTT
Found at i:42571275 original size:21 final size:23
Alignment explanation
Indices: 42571232--42571282 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
42571222 AATGAAAAAA
*
42571232 TTTAGAAGAAAAATCATGTA-TT
1 TTTAGAAAAAAAATCATGTATTT
**
42571254 TTTAGAAAAAAAATTTTG-ATTT
1 TTTAGAAAAAAAATCATGTATTT
42571276 TTTAGAA
1 TTTAGAA
42571283 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (23 bp):
TTTAGAAAAAAAATCATGTATTT
Found at i:42573184 original size:19 final size:19
Alignment explanation
Indices: 42573156--42573198 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
42573146 GAGGTATCAT
42573156 AATTTCTAAT-AGATACCAA
1 AATTTCTAATCA-ATACCAA
*
42573175 AATTTTTAATCAATACC-A
1 AATTTCTAATCAATACCAA
42573193 AATTTC
1 AATTTC
42573199 CAACGCGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 14 0.67
20 1 0.05
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.37
Consensus pattern (19 bp):
AATTTCTAATCAATACCAA
Found at i:42574373 original size:21 final size:22
Alignment explanation
Indices: 42574349--42574395 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
42574339 TATCATGATT
*
42574349 TAAAACCTTAAAAAAT-TTATA
1 TAAAACCATAAAAAATATTATA
*
42574370 TAAAATCATAAAAAATATTATA
1 TAAAACCATAAAAAATATTATA
42574392 -AAAA
1 TAAAA
42574396 TATTTTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAACCATAAAAAATATTATA
Found at i:42574396 original size:21 final size:21
Alignment explanation
Indices: 42574357--42574396 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
42574347 TTTAAAACCT
42574357 TAAAAAATTTATATAAAATCA
1 TAAAAAATTTATATAAAATCA
42574378 TAAAAAATATTATA-AAAAT
1 TAAAAAAT-TTATATAAAAT
42574397 ATTTTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAATTTATATAAAATCA
Found at i:42575537 original size:15 final size:15
Alignment explanation
Indices: 42575492--42575538 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
42575482 CGTCCGGCCC
42575492 AAAACCAAAAATAAA
1 AAAACCAAAAATAAA
*
42575507 TAAA-CAAAACAT--A
1 AAAACCAAAA-ATAAA
42575520 AAAACCAAAAATAAA
1 AAAACCAAAAATAAA
42575535 AAAA
1 AAAA
42575539 AATTCAAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
13 6 0.23
14 10 0.38
15 10 0.38
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAACCAAAAATAAA
Found at i:42576874 original size:18 final size:21
Alignment explanation
Indices: 42576842--42576889 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
42576832 ATGGTGCCTC
*
42576842 TTTATTTACTAAAT-CTT-TTA
1 TTTATTT-TTAAATCCTTGTTA
42576862 TTT-TTTTTAAATCCTTGTTA
1 TTTATTTTTAAATCCTTGTTA
42576882 TTTATTTT
1 TTTATTTT
42576890 CTTTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 5 0.21
19 6 0.25
20 9 0.38
21 4 0.17
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTATTTTTAAATCCTTGTTA
Found at i:42576923 original size:15 final size:16
Alignment explanation
Indices: 42576891--42576931 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
42576881 ATTTATTTTC
*
42576891 TTTATTATTATGCATT
1 TTTATTATTATCCATT
*
42576907 TTTATT-TTATCC-CT
1 TTTATTATTATCCATT
42576921 TTTATTATTAT
1 TTTATTATTAT
42576932 TATTTCTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 7 0.32
15 9 0.41
16 6 0.27
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTATTATTATCCATT
Found at i:42577081 original size:12 final size:12
Alignment explanation
Indices: 42577066--42577090 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42577056 TCTTTTTTAT
42577066 TTTATTTATTCA
1 TTTATTTATTCA
42577078 TTTATTTATTCA
1 TTTATTTATTCA
42577090 T
1 T
42577091 CTATCATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTATTCA
Found at i:42588366 original size:17 final size:17
Alignment explanation
Indices: 42588344--42588396 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
42588334 TAATATTAGT
42588344 TTATTAATATTTTATTA
1 TTATTAATATTTTATTA
***
42588361 TTATTAGCCTTTTATTA
1 TTATTAATATTTTATTA
* *
42588378 TTATTACTA-TATATTA
1 TTATTAATATTTTATTA
42588394 TTA
1 TTA
42588397 CTCTTATTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (17 bp):
TTATTAATATTTTATTA
Found at i:42588382 original size:28 final size:28
Alignment explanation
Indices: 42588343--42588409 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
42588333 TTAATATTAG
* *
42588343 TTTATTAATATT-TTAT-TATTATTAGCCT
1 TTTATTATTATTACTATATATTATTA--CT
42588371 TTTATTATTATTACTATATATTATTACT
1 TTTATTATTATTACTATATATTATTACT
*
42588399 CTTATTATTAT
1 TTTATTATTAT
42588410 AGATTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 23 0.68
29 3 0.09
30 8 0.24
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.61
Consensus pattern (28 bp):
TTTATTATTATTACTATATATTATTACT
Found at i:42588394 original size:13 final size:12
Alignment explanation
Indices: 42588373--42588408 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
42588363 ATTAGCCTTT
42588373 TATTATTATTAC
1 TATTATTATTAC
42588385 TATATATTATTAC
1 TAT-TATTATTAC
*
42588398 TCTTATTATTA
1 TATTATTATTA
42588409 TAGATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:42588425 original size:22 final size:21
Alignment explanation
Indices: 42588346--42588425 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 21
42588336 ATATTAGTTT
*
42588346 ATTAATATTTTATTATTATTAG
1 ATTATTATTTTATTATTA-TAG
* * *
42588368 CCTT-TTATTATTATTACTATAT
1 -ATTATTATT-TTATTATTATAG
*
42588390 ATTATTACTCTTATTATTATAG
1 ATTATTA-TTTTATTATTATAG
42588412 ATTATTATATTTAT
1 ATTATTAT-TTTAT
42588426 CATATTTTCA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
21 3 0.07
22 30 0.68
23 11 0.25
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.59
Consensus pattern (21 bp):
ATTATTATTTTATTATTATAG
Found at i:42594483 original size:12 final size:11
Alignment explanation
Indices: 42594441--42594474 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
42594431 ACTTTGAGTC
*
42594441 AAAAAAATGAT
1 AAAAAAATGAA
*
42594452 GAAAAAATGAA
1 AAAAAAATGAA
42594463 AAAAAAATGAA
1 AAAAAAATGAA
42594474 A
1 A
42594475 GTAAAAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:42595865 original size:50 final size:50
Alignment explanation
Indices: 42595811--42596189 Score: 286
Period size: 50 Copynumber: 7.6 Consensus size: 50
42595801 TGGAACAGAA
* * *
42595811 TAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAAATAT
1 TAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
* * * * * * ** *
42595861 TAAAGCTACAACAGCGAATCTTAC-TCCCTAGGCGA-TGCAGTGGAACAGAT
1 TAAAGCCACATCAGTGAATCTTGCTTCCC-CGAC-ATTGCAGTTAAAAAGAT
* *
42595911 TAAAGCCACATCGGTGAATCTTGCTTCCCCAACATTGCAGTTAAAAAGAT
1 TAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
* * * * * ** *
42595961 TAAAGCTACAACAGCGAATCTTAC-TCCCCAGGAGA-TGCAGTGGAACAGAT
1 TAAAGCCACATCAGTGAATCTTGCTTCCCC--GACATTGCAGTTAAAAAGAT
*
42596011 TAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAATTAAAAAGAT
1 TAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
* * * ** * * * * ** *
42596061 TATAGCTACAACACCGAATCTTAC-TCCCCAAGCGA-CGCAATGGAACAGAT
1 TAAAGCCACATCAGTGAATCTTGCTTCCCCGA-C-ATTGCAGTTAAAAAGAT
* *
42596111 TAAAGCAACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
1 TAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
* * *
42596161 TAAAGCTAAAAT-AGTGAATCTTACTTCCC
1 TAAAGC-CACATCAGTGAATCTTGCTTCCC
42596190 AGGAGGTATA
Statistics
Matches: 247, Mismatches: 69, Indels: 26
0.72 0.20 0.08
Matches are distributed among these distances:
49 20 0.08
50 204 0.83
51 23 0.09
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (50 bp):
TAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
Found at i:42595954 original size:100 final size:100
Alignment explanation
Indices: 42595781--42596252 Score: 653
Period size: 100 Copynumber: 4.7 Consensus size: 100
42595771 AATGCCAGTT
* *
42595781 TTACTTCCCAGGCGATGCAGTGGAACAGAATAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* *
42595846 TGTAGTTAAAAATATTAAAGCTACAACAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* *
42595881 TTACTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCAACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
42595946 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* *
42595981 TTACTCCCCAGGAGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* * *
42596046 TGCAATTAAAAAGATTATAGCTACAACACCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * * *
42596081 TTACTCCCCAAGCGACGCAATGGAACAGATTAAAGCAACATCGGTGAATCTTGCTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* * *
42596146 TGCAGTTAAAAAGATTAAAGCTAAAATAGTGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * * ** * * * * **
42596181 TTACTTCCCAGGAGGTATAGTGGAACCGATTGAAGCTACAGT-AGTGAATCTTATTTCCCCGACA
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACA-TCGGTGAATCTTGCTTCCCCGACA
42596245 -T-CAGTTAA
65 TTGCAGTTAA
42596253 GCAGATCAAA
Statistics
Matches: 332, Mismatches: 39, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
98 7 0.02
99 1 0.00
100 323 0.97
101 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (100 bp):
TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
Found at i:42596912 original size:27 final size:26
Alignment explanation
Indices: 42596844--42596913 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 26
42596834 AATAAGCAGC
42596844 AAATAGAAAGAGAAAAGAAAAATAACA
1 AAATAGAAAG-GAAAAGAAAAATAACA
42596871 AAATAGCAACA-GAAAAGAAAATAGTAGA-A
1 AAATAG-AA-AGGAAAAGAAAA-A-TA-ACA
42596900 AAATAG-AAGGAAAA
1 AAATAGAAAGGAAAA
42596914 ATGGATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
26 1 0.03
27 22 0.59
28 3 0.08
29 10 0.27
30 1 0.03
ACGTcount: A:0.70, C:0.04, G:0.17, T:0.09
Consensus pattern (26 bp):
AAATAGAAAGGAAAAGAAAAATAACA
Done.