Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009019.1 Hibiscus syriacus cultivar Beakdansim tig00112409_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 155641
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:7024 original size:22 final size:23
Alignment explanation
Indices: 6981--7024 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 23
6971 ACTCATCAGG
6981 GTGGTTCTTCATTAATTGCCTTAT
1 GTGGTTC-TCATTAATTGCCTTAT
7005 GTGGTTC-CATTCAATT-CCTT
1 GTGGTTCTCATT-AATTGCCTT
7025 CCCCACTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (23 bp):
GTGGTTCTCATTAATTGCCTTAT
Found at i:7640 original size:4 final size:4
Alignment explanation
Indices: 7626--7655 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
7616 AAAATGTTAG
7626 TAAA GTAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA -TAAA TAAA TAAA TAAA TAAA TAAA T
7656 GACGAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:8659 original size:5 final size:4
Alignment explanation
Indices: 8628--8691 Score: 58
Period size: 4 Copynumber: 15.2 Consensus size: 4
8618 AAAACAAACG
* **
8628 AATA AATAA AATA ATTA AATA AATA AAGTA AA-A AATGTA TGTA AATA
1 AATA AAT-A AATA AATA AATA AATA AA-TA AATA AA--TA AATA AATA
8675 AATA AATA AATA AATA A
1 AATA AATA AATA AATA A
8692 CAACTAGACA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
3 3 0.06
4 37 0.76
5 8 0.16
6 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:8659 original size:26 final size:27
Alignment explanation
Indices: 8628--8688 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
8618 AAAACAAACG
8628 AATAAATAAAAT-AAT-TAAATAAATA
1 AATAAATAAAATGAATGTAAATAAATA
*
8653 AAGT-AA-AAAATGTATGTAAATAAATA
1 AA-TAAATAAAATGAATGTAAATAAATA
8679 AATAAATAAA
1 AATAAATAAA
8689 TAACAACTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
24 5 0.17
25 7 0.23
26 15 0.50
27 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (27 bp):
AATAAATAAAATGAATGTAAATAAATA
Found at i:11191 original size:22 final size:19
Alignment explanation
Indices: 11166--11248 Score: 59
Period size: 19 Copynumber: 4.5 Consensus size: 19
11156 CTTAATGTCC
11166 ATCGCAACGCGGAAACGACAAA
1 ATCGCAACGC-GAAACG--AAA
* *
11188 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAACGAAA
*
11207 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAACGAAA
* *
11221 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAACGAAA
11240 ATCGCAACG
1 ATCGCAACG
11249 AGGGAATCGC
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.41
21 5 0.10
22 9 0.18
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAACGAAA
Found at i:11209 original size:19 final size:19
Alignment explanation
Indices: 11185--11284 Score: 87
Period size: 19 Copynumber: 5.8 Consensus size: 19
11175 CGGAAACGAC
11185 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
11204 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATG
*
11218 AGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
11237 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATG
**
11251 GGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
11270 -AAATCGCAACGCGAA
1 AAAATCGCAATGCGAA
11285 TTTAATTTCG
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
14 19 0.29
15 2 0.03
16 4 0.06
17 4 0.06
18 15 0.23
19 21 0.32
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:11224 original size:33 final size:33
Alignment explanation
Indices: 11187--11280 Score: 172
Period size: 33 Copynumber: 2.9 Consensus size: 33
11177 GAAACGACAA
11187 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
11220 AATCGCAATGCGAAATGAAAATCGCAACGAGGG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
11253 AATCGCAATGCGAAATG-AAATCGCAACG
1 AATCGCAATGCGAAATGAAAATCGCAACG
11281 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 11 0.18
33 49 0.82
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:11302 original size:19 final size:20
Alignment explanation
Indices: 11280--11322 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
11270 AAATCGCAAC
11280 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
11299 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
11319 GCGA
1 GCGA
11323 TTCACTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:11482 original size:14 final size:14
Alignment explanation
Indices: 11463--11499 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
11453 CATCAATTAA
11463 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
11477 ACAAATCACCTTTT
1 ACAAATCAACTTTT
11491 ACAAATCAA
1 ACAAATCAA
11500 TTAAACATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:12929 original size:42 final size:42
Alignment explanation
Indices: 12883--12966 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
12873 CGATGACAGT
* * *
12883 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
12925 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
12967 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:15048 original size:33 final size:33
Alignment explanation
Indices: 14991--15089 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
14981 ACGAGATAAT
*
14991 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
15025 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
15058 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
15090 GCGAAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:15083 original size:19 final size:19
Alignment explanation
Indices: 14966--15188 Score: 241
Period size: 19 Copynumber: 12.1 Consensus size: 19
14956 TCTTTTGGTT
*
14966 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
14985 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
15005 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
15023 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
15039 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
15057 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
15072 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
15092 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
15111 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
15130 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
15149 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
*
15168 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
15187 GA
1 GA
15189 TTTTGGTTTC
Statistics
Matches: 176, Mismatches: 15, Indels: 26
0.81 0.07 0.12
Matches are distributed among these distances:
14 19 0.11
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.02
19 100 0.57
20 45 0.26
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:15217 original size:19 final size:19
Alignment explanation
Indices: 15184--15228 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
15174 AAAATCGCAA
*
15184 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
15203 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
15222 TGCGATT
1 TGCGATT
15229 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:15878 original size:20 final size:20
Alignment explanation
Indices: 15785--15878 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
15775 CGCTAAGTAA
*
15785 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
15805 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
15825 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
15846 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
15866 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
15879 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:15897 original size:41 final size:41
Alignment explanation
Indices: 15806--15940 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
15796 AAAGTCAGTA
* * * ** *
15806 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
15846 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
15888 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
15929 TCGCGTTGCGAT
1 TCGCGTTGCGAT
15941 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:15911 original size:20 final size:20
Alignment explanation
Indices: 15867--15959 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
15857 ATAGTCAGTA
* **
15867 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
15888 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
15908 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
15929 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
15949 TCGCATTGCGA
1 TCGCATTGCGA
15960 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:15941 original size:41 final size:41
Alignment explanation
Indices: 15867--15962 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
15857 ATAGTCAGTA
*
15867 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
15908 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
15949 TCGCATTGCGAATT
1 TCGCATTGCGAATT
15963 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:16867 original size:14 final size:14
Alignment explanation
Indices: 16848--16885 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
16838 TCTAGTTATT
16848 AAATTAAAATTTCA
1 AAATTAAAATTTCA
16862 AAATTAAAATTTCA
1 AAATTAAAATTTCA
16876 AAATTAAAAT
1 AAATTAAAAT
16886 AGAAATAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATTAAAATTTCA
Found at i:31858 original size:27 final size:27
Alignment explanation
Indices: 31828--31883 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
31818 TACAATGCCA
*
31828 AAGATTTCAACAATTGAGGATGTTGAG
1 AAGATTTCAACAATTGAAGATGTTGAG
31855 AAGATTTCAACAATTGAAGATGTTGAG
1 AAGATTTCAACAATTGAAGATGTTGAG
31882 AA
1 AA
31884 CATTGACTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (27 bp):
AAGATTTCAACAATTGAAGATGTTGAG
Found at i:42308 original size:3 final size:3
Alignment explanation
Indices: 42300--42362 Score: 60
Period size: 3 Copynumber: 22.0 Consensus size: 3
42290 AAAATAAAAT
* * * *
42300 TAA TAA TAA TAA T-C TAT TAT TAA TAA TAA TAA T-A TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
42346 T-A TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
42363 ATAAAAAAGA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
2 5 0.10
3 45 0.90
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:42336 original size:11 final size:10
Alignment explanation
Indices: 42291--42366 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
42281 ATTTCAAGAA
42291 AAATAA-AAT
1 AAATAATAAT
*
42300 TAATAATAAT
1 AAATAATAAT
* *
42310 -AATCTATTAT
1 AAAT-AATAAT
*
42320 TAATAATAAT
1 AAATAATAAT
42330 AATATAATAA-
1 AA-ATAATAAT
*
42340 AAATAATATAA
1 AAATAATA-AT
42351 AAATAATAAT
1 AAATAATAAT
42361 AAATAA
1 AAATAA
42367 AAAAGACAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
9 14 0.26
10 22 0.41
11 18 0.33
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (10 bp):
AAATAATAAT
Found at i:42337 original size:14 final size:14
Alignment explanation
Indices: 42320--42366 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
42310 AATCTATTAT
42320 TAATAATAATAATA
1 TAATAATAATAATA
*
42334 TAATAAAAATAATA
1 TAATAATAATAATA
*
42348 TAAAAATAATAATA
1 TAATAATAATAATA
42362 -AATAA
1 TAATAA
42367 AAAAGACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 4 0.14
14 25 0.86
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:42344 original size:17 final size:17
Alignment explanation
Indices: 42289--42370 Score: 54
Period size: 17 Copynumber: 5.2 Consensus size: 17
42279 ATATTTCAAG
42289 AAAAATAA-AAT-TAAT
1 AAAAATAATAATATAAT
* * *
42304 AATAATAAT-CTATTATT
1 AAAAATAATAATA-TAAT
*
42321 AATAATAATAATATAAT
1 AAAAATAATAATATAAT
42338 AAAAATAAT-ATA-AA-
1 AAAAATAATAATATAAT
*
42352 AATAATAATAA-ATAA-
1 AAAAATAATAATATAAT
42367 AAAA
1 AAAA
42371 GACAAAAACA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
14 9 0.17
15 16 0.30
16 3 0.06
17 23 0.43
18 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAATAATAATATAAT
Found at i:42957 original size:28 final size:28
Alignment explanation
Indices: 42917--42976 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
42907 AAGAATGTGA
*
42917 TCAGTCAAGAAGGAGATGACCACCTCAT
1 TCAGTCAAGAAGGAGATGACCACATCAT
* *
42945 TCAGTTAAGAAGGAGATGATCACATCAT
1 TCAGTCAAGAAGGAGATGACCACATCAT
42973 TCAG
1 TCAG
42977 AAGAGGCACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (28 bp):
TCAGTCAAGAAGGAGATGACCACATCAT
Found at i:43340 original size:53 final size:52
Alignment explanation
Indices: 43262--43406 Score: 211
Period size: 53 Copynumber: 2.8 Consensus size: 52
43252 GGTCCATATT
* * *
43262 ATCCATGT-GGATATCTTGAAAGCTCACATCAGCATGAAAAAAACAGAAGTA
1 ATCCATGTGGGGTATCTTGAAGGCTCACATCAGCATGAAAAAAACAAAAGTA
*
43313 ATCCATGTGGGGGTATCTTGAAGGCTCACATCAGCATGAAAAAGACAAAAGTA
1 ATCCATGT-GGGGTATCTTGAAGGCTCACATCAGCATGAAAAAAACAAAAGTA
* * *
43366 ATCCATGTGGGGCATCTTGAAGGCTCACACCAGTATGAAAA
1 ATCCATGTGGGGTATCTTGAAGGCTCACATCAGCATGAAAA
43407 TGTTGGATAT
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
51 8 0.09
52 30 0.35
53 47 0.55
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (52 bp):
ATCCATGTGGGGTATCTTGAAGGCTCACATCAGCATGAAAAAAACAAAAGTA
Found at i:45519 original size:2 final size:2
Alignment explanation
Indices: 45512--45539 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45502 TCACTAATTA
45512 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
45540 TTAAGGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46045 original size:12 final size:13
Alignment explanation
Indices: 46014--46047 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
46004 TTATTATCCC
46014 TTTTATTTTAATA
1 TTTTATTTTAATA
*
46027 TTTTATTTTATTA
1 TTTTATTTTAATA
46040 -TTTATTTT
1 TTTTATTTT
46048 TTAGTCCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTTAATA
Found at i:46410 original size:3 final size:3
Alignment explanation
Indices: 46396--46441 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
46386 TCTTTTTTAT
* * *
46396 TTA TTT TTA TTA TTA -TA TTA TTA TTA TTA ATA -GA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46442 ATTTTGTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
2 3 0.08
3 33 0.92
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:46419 original size:14 final size:14
Alignment explanation
Indices: 46392--46441 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
46382 TCCGTCTTTT
*
46392 TTATT-TATTTTTA
1 TTATTATATTATTA
46405 TTATTATATTATTA
1 TTATTATATTATTA
46419 TTATTAATAGATTATTA
1 TTATT-AT--ATTATTA
46436 TTATTA
1 TTATTA
46442 ATTTTGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 5 0.16
14 12 0.38
15 2 0.06
16 1 0.03
17 12 0.38
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
TTATTATATTATTA
Found at i:46442 original size:17 final size:17
Alignment explanation
Indices: 46396--46443 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
46386 TCTTTTTTAT
* * *
46396 TTATTTTTATTATTATA
1 TTATTATTATTAATAGA
46413 TTATTATTATTAATAGA
1 TTATTATTATTAATAGA
46430 TTATTATTATTAAT
1 TTATTATTATTAAT
46444 TTTGTTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TTATTATTATTAATAGA
Found at i:54877 original size:345 final size:344
Alignment explanation
Indices: 54185--55525 Score: 2173
Period size: 345 Copynumber: 4.0 Consensus size: 344
54175 CATTCTATTC
54185 GGGGGGGGGGGGGGGCTTTCAGGATTTAGGGACCTTAAGTTTAAGGGCAAGAAACTCGAGAAGGA
1 GGGGGGGGGGGGGGGCTTTCAGGATTTAGGGACCTTAAGTTTAAGGGCAAGAAACTCGAGAAGGA
54250 ATTGTTTGGTTTCATAGAAACTTTGTATATTAGTGTTATCATATTTTATATACTTAATACAATTA
66 ATTGTTTGGTTTCATAGAAACTTTGTATATTAGTGTTATCATATTTTATATACTTAATACAATTA
54315 ATTGTACAAAATATATTTAAAGTTGACAATTAAGTGACATGTGTCATACTCATAAATTTTAAAAA
131 ATTGTACAAAATATATTTAAAGTTGACAATTAAGTGACATGTGTCATACTCATAAATTTTAAAAA
54380 AATTATTATAAAATAAAAAACTTAAAATTATAATTTATTTTTAAAAAAAATCACAAATTTCTTTA
196 AATTATTATAAAATAAAAAACTTAAAATTATAATTTATTTTT-AAAAAAATCACAAATTTCTTTA
* * * *
54445 AAATTATAATGAAAATTTCAAAAACTCTAAAATCTTTAATTTTAAATTCATTTTCAACCGATGTG
260 AAATCATAATGAAAAATTCAAAAACCCTAAAATCTTTAATTTCAAATTCATTTTCAACCGATGTG
54510 GATTATCATTCTATTCGGGG
325 GATTATCATTCTATTCGGGG
54530 GGGGGGGGGGGGGGGCTTTCAGGATTTAGGGACCTTAAGTTTAAGGGCAAGAAACTCGAGAAGGA
1 GGGGGGGGGGGGGGGCTTTCAGGATTTAGGGACCTTAAGTTTAAGGGCAAGAAACTCGAGAAGGA
54595 ATTGTTTGGTTTCATAGAAACTTTGTATATTAGTGTTATCATATTTTATATACTTAATACAATTA
66 ATTGTTTGGTTTCATAGAAACTTTGTATATTAGTGTTATCATATTTTATATACTTAATACAATTA
54660 ATTGTACAAAATATATTTAAAGTTGACAATTAAGTGACATGTGTCATACTCATAAATTTTAAAAA
131 ATTGTACAAAATATATTTAAAGTTGACAATTAAGTGACATGTGTCATACTCATAAATTTTAAAAA
54725 AATTATTATAAAATAAAAAACTTAAAATTATAATTTATTTTTAAAAAAATCACAAATTTCTTTAA
196 AATTATTATAAAATAAAAAACTTAAAATTATAATTTATTTTTAAAAAAATCACAAATTTCTTTAA
* * *
54790 AATTATAATGAAAATTTCAAAAACCCTAAAATCTTTAATTTTAAATTCATTTTCAACCGATGTGG
261 AATCATAATGAAAAATTCAAAAACCCTAAAATCTTTAATTTCAAATTCATTTTCAACCGATGTGG
54855 ATTATCATTCTATTC----
326 ATTATCATTCTATTCGGGG
*
54870 -GGGGGGGGGGGGGG-TTTCAGGATTTAGGGACCTTAAGTTTAA-GGCAAGAAAGTCGAGAAGGA
1 GGGGGGGGGGGGGGGCTTTCAGGATTTAGGGACCTTAAGTTTAAGGGCAAGAAACTCGAGAAGGA
54932 ATTGTTTGGTTTCATAGAAACTTTGTATATTAGTGTTATCATATTTTATATACTTAATACAATTA
66 ATTGTTTGGTTTCATAGAAACTTTGTATATTAGTGTTATCATATTTTATATACTTAATACAATTA
* * * *
54997 ATTGTCCAAAATATATTTAAAGTTGACAGTTAAGTGACATCTGTCATACTCATAAA-TTCAAAAA
131 ATTGTACAAAATATATTTAAAGTTGACAATTAAGTGACATGTGTCATACTCATAAATTTTAAAAA
*
55061 AA-TATTATAAAATAAAAAACTTAAAATTATAATTTATTTTT--AAATATCACAAATTTCTTTAA
196 AATTATTATAAAATAAAAAACTTAAAATTATAATTTATTTTTAAAAAAATCACAAATTTCTTTAA
* *
55123 AATCATAATAAAAAATTCAAAAACTCTAAAATCTTTAATTTCAAATTCATTTTCAA-C-------
261 AATCATAATGAAAAATTCAAAAACCCTAAAATCTTTAATTTCAAATTCATTTTCAACCGATGTGG
55180 -----CA--C-A-T-GGGG
326 ATTATCATTCTATTCGGGG
* **
55189 GGGGGGATTGGGGGGCCCTTTCAGGATTTAGGGACCTTAAGTTTAAGGGCAAGAAACTCGAGAAG
1 GGGGGG--GGGGGGGGGCTTTCAGGATTTAGGGACCTTAAGTTTAAGGGCAAGAAACTCGAGAAG
55254 GAATTGTTTGGTTTCATAGAAACTTTGTATATTAGTGTTATCATATTTTATATACTTAATACAAT
64 GAATTGTTTGGTTTCATAGAAACTTTGTATATTAGTGTTATCATATTTTATATACTTAATACAAT
* * *
55319 TAATTGTCCAAAATATATTTAAAGTTGGCAGTTAAGTGACATGTGTCATACTCATAAATTTTAAA
129 TAATTGTACAAAATATATTTAAAGTTGACAATTAAGTGACATGTGTCATACTCATAAATTTT--A
*
55384 AAAAAAATATTATAAAATAAAAAAACTTAAAATTATAATTTATTTTTAAAAAAATCACAAATTTC
192 AAAAAATTATTATAAAAT-AAAAAACTTAAAATTATAATTTATTTTTAAAAAAATCACAAATTTC
* * * * *
55449 TTTAAAATCATAATGAAAAAAATCAAAAACCCGAAAATATTTAATTTCAAATTCATTATCAACAG
256 TTTAAAATCATAATG-AAAAATTCAAAAACCCTAAAATCTTTAATTTCAAATTCATTTTCAACCG
55514 ATGTGGATTATC
320 ATGTGGATTATC
55526 TCTCGTCACT
Statistics
Matches: 939, Mismatches: 27, Indels: 60
0.92 0.03 0.06
Matches are distributed among these distances:
316 1 0.00
317 1 0.00
318 1 0.00
320 7 0.01
322 6 0.01
323 28 0.03
324 138 0.15
325 2 0.00
327 7 0.01
328 11 0.01
329 28 0.03
331 29 0.03
332 42 0.04
333 71 0.08
335 39 0.04
336 9 0.01
337 137 0.15
338 28 0.03
339 14 0.01
344 102 0.11
345 238 0.25
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (344 bp):
GGGGGGGGGGGGGGGCTTTCAGGATTTAGGGACCTTAAGTTTAAGGGCAAGAAACTCGAGAAGGA
ATTGTTTGGTTTCATAGAAACTTTGTATATTAGTGTTATCATATTTTATATACTTAATACAATTA
ATTGTACAAAATATATTTAAAGTTGACAATTAAGTGACATGTGTCATACTCATAAATTTTAAAAA
AATTATTATAAAATAAAAAACTTAAAATTATAATTTATTTTTAAAAAAATCACAAATTTCTTTAA
AATCATAATGAAAAATTCAAAAACCCTAAAATCTTTAATTTCAAATTCATTTTCAACCGATGTGG
ATTATCATTCTATTCGGGG
Found at i:58336 original size:3 final size:3
Alignment explanation
Indices: 58328--58373 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
58318 GTATAATTTT
* *
58328 ATA ATA ATA ATA AAA ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
58374 ACTCAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:58824 original size:16 final size:17
Alignment explanation
Indices: 58793--58825 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58783 TATCTTGGAG
*
58793 TTTTATTTTTATAATTT
1 TTTTATTTCTATAATTT
58810 TTTTATTTCTA-AATTT
1 TTTTATTTCTATAATTT
58826 ATAATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTTCTATAATTT
Found at i:63810 original size:33 final size:33
Alignment explanation
Indices: 63765--63835 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
63755 TCAATCATCA
*
63765 TTCACGATAATATCAATACCAAAACATTCATAT
1 TTCACGATAATATCAATACCAAAACATTCACAT
* *
63798 TTCAC-ATCAATATCGATACCAAAATATTCACAT
1 TTCACGAT-AATATCAATACCAAAACATTCACAT
63831 TTCAC
1 TTCAC
63836 TTATCTTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.42, C:0.24, G:0.03, T:0.31
Consensus pattern (33 bp):
TTCACGATAATATCAATACCAAAACATTCACAT
Found at i:64679 original size:29 final size:29
Alignment explanation
Indices: 64646--64704 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
64636 AGCACCGCGT
64646 ATTCAAGAGTATAAACATTCGTTGTCATA
1 ATTCAAGAGTATAAACATTCGTTGTCATA
64675 ATTCAAGAGTATAAACATTCGTTGTCATA
1 ATTCAAGAGTATAAACATTCGTTGTCATA
64704 A
1 A
64705 GATCGAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (29 bp):
ATTCAAGAGTATAAACATTCGTTGTCATA
Found at i:65200 original size:18 final size:19
Alignment explanation
Indices: 65179--65215 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
65169 AATATCAAAC
65179 AATAACAAAACTAA-AAAA
1 AATAACAAAACTAATAAAA
65197 AATAACAAAACTAATAAAA
1 AATAACAAAACTAATAAAA
65216 CACCATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.14
Consensus pattern (19 bp):
AATAACAAAACTAATAAAA
Found at i:65705 original size:31 final size:30
Alignment explanation
Indices: 65667--65753 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 30
65657 GTATCAAAAG
*
65667 TTATAAAATAATCATTAAAATTCTTAAATAA
1 TTATAAAAT-ATCATTAAAATTATTAAATAA
** *
65698 TTATAAAATTATCATTAATTTTTATTAAATTA
1 TTATAAAA-TATCATTAA-AATTATTAAATAA
*
65730 TTATAAAATATCATTAAATTTATT
1 TTATAAAATATCATTAAAATTATT
65754 GAGCTATTAC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
30 6 0.12
31 25 0.51
32 18 0.37
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
TTATAAAATATCATTAAAATTATTAAATAA
Found at i:65750 original size:32 final size:32
Alignment explanation
Indices: 65667--65750 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
65657 GTATCAAAAG
* *
65667 TTATAAAATAATCATTAAA--ATTCTTAAATAA
1 TTATAAAAT-ATCATTAAATTTTTATTAAATAA
*
65698 TTATAAAATTATCATT-AATTTTTATTAAATTA
1 TTATAAAA-TATCATTAAATTTTTATTAAATAA
65730 TTATAAAATATCATTAAATTT
1 TTATAAAATATCATTAAATTT
65751 ATTGAGCTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
30 2 0.04
31 21 0.46
32 23 0.50
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
TTATAAAATATCATTAAATTTTTATTAAATAA
Found at i:67174 original size:25 final size:27
Alignment explanation
Indices: 67128--67201 Score: 89
Period size: 25 Copynumber: 2.8 Consensus size: 27
67118 GGATGCAAAG
* * *
67128 TTTTATATTAAAAGATAAATTTATAAAA
1 TTTTA-ATAAAAAAATATATTTATAAAA
*
67156 TTTT-A-AAAAATATATATTTATAAAA
1 TTTTAATAAAAAAATATATTTATAAAA
67181 TTTTAATAAAAAAATATATTT
1 TTTTAATAAAAAAATATATTT
67202 TCAACAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 21 0.52
26 2 0.05
27 13 0.32
28 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (27 bp):
TTTTAATAAAAAAATATATTTATAAAA
Found at i:70982 original size:24 final size:25
Alignment explanation
Indices: 70955--71006 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
70945 TCATTTAAAG
70955 TTTTTA-AAATA-TATTTTTTCATA
1 TTTTTATAAATAGTATTTTTTCATA
*
70978 TTTTTATTAATAGTATTTTTTCATA
1 TTTTTATAAATAGTATTTTTTCATA
71003 TTTT
1 TTTT
71007 CTATTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 6 0.23
24 4 0.15
25 16 0.62
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTTATAAATAGTATTTTTTCATA
Found at i:71000 original size:25 final size:25
Alignment explanation
Indices: 70962--71011 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
70952 AAGTTTTTAA
70962 AATATATTTTTTCATATTTT-TATT
1 AATATATTTTTTCATATTTTCTATT
70986 AATAGTATTTTTTCATATTTTCTATT
1 AATA-TATTTTTTCATATTTTCTATT
71012 CAAAATATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 4 0.17
25 16 0.67
26 4 0.17
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (25 bp):
AATATATTTTTTCATATTTTCTATT
Found at i:79537 original size:28 final size:28
Alignment explanation
Indices: 79492--79546 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
79482 CACACGTTGC
* * * *
79492 TTTCAAGCATTTGTTCGACGATATAATG
1 TTTCAAGCAATAGCTCGACGACATAATG
79520 TTTCAAGCAATAGCTCGACGACATAAT
1 TTTCAAGCAATAGCTCGACGACATAAT
79547 ATAAACTGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (28 bp):
TTTCAAGCAATAGCTCGACGACATAATG
Found at i:97639 original size:21 final size:22
Alignment explanation
Indices: 97599--97653 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
97589 TTTTTTATAT
* **
97599 ATTATTTTTTTTCAATTAAATC
1 ATTATTTTTATTCAATTAAAAA
*
97621 ATTATTTTTATTGAA-TAAAAA
1 ATTATTTTTATTCAATTAAAAA
*
97642 AATATTTTTATT
1 ATTATTTTTATT
97654 ATTATTTCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTATTTTTATTCAATTAAAAA
Found at i:101067 original size:2 final size:2
Alignment explanation
Indices: 101060--101088 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
101050 AAAACCCTTA
101060 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
101089 AAGAAAAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:103022 original size:30 final size:30
Alignment explanation
Indices: 102971--103031 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
102961 TAAATTCATC
*
102971 AAAAAAATTAAACATGAAATAA-ATTAGAA
1 AAAAAAATCAAACATGAAATAACATTAGAA
* * *
103000 AAAAAAATCAAATATGTTAATAACATTCGAA
1 AAAAAAATCAAACATG-AAATAACATTAGAA
103031 A
1 A
103032 CTTTCTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 14 0.54
30 5 0.19
31 7 0.27
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.23
Consensus pattern (30 bp):
AAAAAAATCAAACATGAAATAACATTAGAA
Found at i:104886 original size:24 final size:25
Alignment explanation
Indices: 104851--104906 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
104841 TTTAATTTAA
*
104851 TATATAAA-TTTTAA-AAAATATATT
1 TATAAAAACTTTTAATAAAAT-TATT
*
104875 T-TAAAAACTTTTAATTAAATTATT
1 TATAAAAACTTTTAATAAAATTATT
104899 TATAAAAA
1 TATAAAAA
104907 AATATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 12 0.44
25 10 0.37
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
TATAAAAACTTTTAATAAAATTATT
Found at i:105744 original size:2 final size:2
Alignment explanation
Indices: 105739--105769 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
105729 ATTGTTTTAT
105739 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 T
105770 GATGACGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:113900 original size:110 final size:108
Alignment explanation
Indices: 113777--113998 Score: 299
Period size: 112 Copynumber: 2.0 Consensus size: 108
113767 TTATGACACT
*
113777 ATGGGAATGCTCGGCGTCTTCAAGTAATT-GG-C-CT-GTGGGATATCTCGGCGTCTTCTGCATG
1 ATGGGAATGCTCGGCGTCTTCAAGCAATTGGGACTCTGGTGGGATATCTCGGCGTCTTCTGCA--
113838 CTACAAGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
64 -T---AGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
* *
113887 ATGGGAATGCTCGGTGTCTTCAAGCAATTGGGATCTCTCGGAGTGGGATCTCTCGGCGTCTTCTG
1 ATGGGAATGCTCGGCGTCTTCAAGCAATTGGGA-CTCT--G-GTGGGATATCTCGGCGTCTTCTG
113952 CATAGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
62 CATAGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
113999 GCGGGAATCT
Statistics
Matches: 101, Mismatches: 3, Indels: 14
0.86 0.03 0.12
Matches are distributed among these distances:
110 27 0.27
111 2 0.02
112 44 0.44
113 1 0.01
114 2 0.02
115 1 0.01
118 24 0.24
ACGTcount: A:0.17, C:0.24, G:0.30, T:0.29
Consensus pattern (108 bp):
ATGGGAATGCTCGGCGTCTTCAAGCAATTGGGACTCTGGTGGGATATCTCGGCGTCTTCTGCATA
GGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
Found at i:114282 original size:18 final size:18
Alignment explanation
Indices: 114259--114305 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
114249 CTTTGTGTCC
114259 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
114277 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
114295 GAAGCGTGAGA
1 GAAGCGTGAGA
114306 CTAATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (18 bp):
GAAGCGTGAGATTCGTCT
Found at i:117698 original size:8 final size:8
Alignment explanation
Indices: 117687--118337 Score: 383
Period size: 8 Copynumber: 86.8 Consensus size: 8
117677 ATTATTTAAC
117687 TTTAATGA
1 TTTAATGA
117695 TTTAAT-A
1 TTTAATGA
* *
117702 -ATAATTA
1 TTTAATGA
*
117709 TTTAA--C
1 TTTAATGA
117715 TTTAATGA
1 TTTAATGA
117723 TTTAAT-A
1 TTTAATGA
* *
117730 -ATAATTA
1 TTTAATGA
*
117737 TTTAA--C
1 TTTAATGA
117743 TTTAATGA
1 TTTAATGA
117751 TTTAAT-A
1 TTTAATGA
* *
117758 -ATAATTA
1 TTTAATGA
117765 CTTTAATGA
1 -TTTAATGA
*
117774 TTTAA--C
1 TTTAATGA
117780 TTTAATGA
1 TTTAATGA
*
117788 TTTAATAATAA
1 -TT--TAATGA
117799 TTTAAT--
1 TTTAATGA
117805 TTTAATGA
1 TTTAATGA
117813 TTTAAT-A
1 TTTAATGA
* *
117820 -ATAATTA
1 TTTAATGA
117827 CTTTAATGA
1 -TTTAATGA
117836 TTTAAT--
1 TTTAATGA
117842 TTTAATGA
1 TTTAATGA
117850 TTTAATGA
1 TTTAATGA
*
117858 TTTAA--C
1 TTTAATGA
117864 TTTAATGA
1 TTTAATGA
117872 TTTAAT-A
1 TTTAATGA
* *
117879 -ATAATTA
1 TTTAATGA
117886 CTTTAATGA
1 -TTTAATGA
117895 TTTAAT--
1 TTTAATGA
117901 TTTAATGA
1 TTTAATGA
117909 TTTAAT-A
1 TTTAATGA
* *
117916 -ATAATTA
1 TTTAATGA
117923 CTTTAATGA
1 -TTTAATGA
*
117932 TTTAA--C
1 TTTAATGA
117938 TTTAATGA
1 TTTAATGA
117946 TTTAAT-A
1 TTTAATGA
* *
117953 -ATAATTA
1 TTTAATGA
117960 CTTTAATGA
1 -TTTAATGA
117969 TTTAATGA
1 TTTAATGA
*
117977 TTTAA--C
1 TTTAATGA
117983 TTTAATGA
1 TTTAATGA
117991 TTTAAT-A
1 TTTAATGA
* *
117998 -ATAATTA
1 TTTAATGA
118005 CTTTAATGA
1 -TTTAATGA
*
118014 TTTAA--C
1 TTTAATGA
118020 TTTAATGA
1 TTTAATGA
118028 TTTAAT-A
1 TTTAATGA
* *
118035 -ATAATTA
1 TTTAATGA
118042 CTTTAATGA
1 -TTTAATGA
118051 TTTAATGA
1 TTTAATGA
118059 TTTAATGA
1 TTTAATGA
118067 TTTAAT-A
1 TTTAATGA
* *
118074 -ATAATTA
1 TTTAATGA
118081 CTTTAATGA
1 -TTTAATGA
118090 TTTAATGA
1 TTTAATGA
*
118098 TTTAATAA
1 TTTAATGA
118106 TTTAATGA
1 TTTAATGA
118114 TTTAATGA
1 TTTAATGA
118122 TTTAAT-A
1 TTTAATGA
* *
118129 -ATAATTA
1 TTTAATGA
118136 CTTTAATGA
1 -TTTAATGA
*
118145 TTTAA--C
1 TTTAATGA
118151 TTTAATGA
1 TTTAATGA
118159 TTTAAT-A
1 TTTAATGA
* *
118166 -ATAATTA
1 TTTAATGA
118173 CTTTAATGA
1 -TTTAATGA
118182 TTTAATGA
1 TTTAATGA
118190 TTTAATGA
1 TTTAATGA
118198 TTTAATGA
1 TTTAATGA
118206 TTTAAT-A
1 TTTAATGA
* *
118213 -ATAATTA
1 TTTAATGA
118220 TTTTAATGA
1 -TTTAATGA
118229 TTTAATGA
1 TTTAATGA
118237 TTTAATGA
1 TTTAATGA
118245 TTTAATGA
1 TTTAATGA
118253 TTTAAT-A
1 TTTAATGA
* *
118260 -ATAATTA
1 TTTAATGA
118267 CTTTAATGA
1 -TTTAATGA
118276 TTTAAT--
1 TTTAATGA
*
118282 TTTAATAA
1 TTTAATGA
118290 TTTAAT-A
1 TTTAATGA
* *
118297 -ATAATTA
1 TTTAATGA
*
118304 CTTAAT--
1 TTTAATGA
118310 TTTAATGA
1 TTTAATGA
118318 TTTAAT--
1 TTTAATGA
118324 TTTAATGA
1 TTTAATGA
118332 TTTAAT
1 TTTAAT
118338 AATAATTACT
Statistics
Matches: 508, Mismatches: 62, Indels: 146
0.71 0.09 0.20
Matches are distributed among these distances:
6 135 0.27
7 30 0.06
8 274 0.54
9 62 0.12
10 2 0.00
11 5 0.01
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (8 bp):
TTTAATGA
Found at i:117778 original size:37 final size:37
Alignment explanation
Indices: 117731--118348 Score: 569
Period size: 37 Copynumber: 16.0 Consensus size: 37
117721 GATTTAATAA
*
117731 TAATTATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
117768 TAATGATTTAACTTTAATGATTTAATAATAATTTAATTT
1 TAATGATTTAACTTTAATGATTTAATAATAA-TT-ACTT
** *
117807 TAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGA-TT
1 TAATGA--T--T--T-A--ACTTTAATGATTTAATAATAATTACTT
117852 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
117889 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
117926 TAATGATTTAACTTTAATGATTTAATAATAATTACTTTAATGATT
1 TAATGATTTAACTTTAATGATTTAATAATAATTAC--------TT
117971 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
118008 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
118045 TAATGATTTAATGATTTAATGATTTAATAATAATTACTT
1 TAATGATTTAA--CTTTAATGATTTAATAATAATTACTT
* * * *
118084 TAATGATTTAATGATTTAATAATTTAATGATTTAATGA-TT
1 TAATGATTTAA--CTTTAATGATTTAAT-A-ATAATTACTT
* * *
118124 TAATAATAATT-ACTTTAATGATTTAACT-TTAATGA-TT
1 TAATGAT--TTAACTTTAATGATTTAA-TAATAATTACTT
* * *
118161 TAATAATAATT-ACTTTAATGATTTAATGATTTAATGA-TT
1 TAATGAT--TTAACTTTAATGATTTAAT-A-ATAATTACTT
* ** *
118200 TAATGATTTAA---TAAT-AATT-ATTTTAATGA-TT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
118231 TAATGATTTAATGATTTAATGATTTAATAATAATTACTT
1 TAATGATTTAA--CTTTAATGATTTAATAATAATTACTT
* *
118270 TAATGATTTAATTTTAATAATTTAATAATAATTACTTAATTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTAC-----TT
*
118312 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
118349 GACTTTAATG
Statistics
Matches: 510, Mismatches: 27, Indels: 88
0.82 0.04 0.14
Matches are distributed among these distances:
31 20 0.04
33 2 0.00
34 3 0.01
35 4 0.01
36 26 0.05
37 216 0.42
38 11 0.02
39 102 0.20
40 10 0.02
41 8 0.02
42 38 0.07
43 2 0.00
45 46 0.09
46 2 0.00
47 1 0.00
48 19 0.04
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (37 bp):
TAATGATTTAACTTTAATGATTTAATAATAATTACTT
Found at i:118139 original size:131 final size:128
Alignment explanation
Indices: 117731--118323 Score: 630
Period size: 131 Copynumber: 4.7 Consensus size: 128
117721 GATTTAATAA
* *
117731 TAATTATTTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAA-CTTTAATGATTTAATA
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAATATTTAATGATTTAATA
* * ** *
117795 AT-A--A-TTTAAT--TTTAATGATTTAATAATAATT-ACTTTAATGATTTAATTTTAATGA-TT
66 ATAATTACTTTAATGATTTAATGATTTAATGAT--TTAAATTTAATGATTTAATAATAATTACTT
117852 TAATGATTTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAAT-TTTAATGATTTAATA
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAATATTTAATGATTTAATA
* * * * *
117916 ATAATTACTTTAATGATTTAA--CTTTAATGATTT-AA--TAAT-AATTACT-TTAATGA-TT
66 ATAATTACTTTAATGATTTAATGATTTAATGATTTAAATTTAATGATTTAATAATAATTACTT
*
117971 TAATGATTTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAA-CTTTAATGATTTAATA
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAATATTTAATGATTTAATA
* * * *
118035 ATAATTACTTTAATGATTTAATGATTTAATGATTT-AATAATAATTACTTTAATGATTTAATGA-
66 ATAATTACTTTAATGATTTAATGATTTAATGATTTAAAT-TTAATGA-TTTAAT-A-ATAATTAC
118098 TT
127 TT
* * *
118100 TAATAATTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAA-CTTTAATGATTTAA
1 TAATGATTTAA--CTTTAATGATTTAATAATAATTACTTTAATGATTTAATATTTAATGATTTAA
* ** *
118164 TAATAATTACTTTAATGATTTAATGATTTAATGATTTAATGATTTAATAATAATT-ATTTTAATG
64 TAATAATTACTTTAATGATTTAATGATTTAATGATTTAA--ATTTAATGAT--TTAATAATAATT
118228 A-TT
125 ACTT
* *
118231 TAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAAT-TTTAATAATTTAA
1 TAATGATTTAA--CTTTAATGATTTAATAATAATTACTTTAATGATTTAATATTTAATGATTTAA
118295 TAATAATTAC-TTAAT--TTTAATGATTTAAT
64 TAATAATTACTTTAATGATTTAATGATTTAAT
118324 TTTAATGATT
Statistics
Matches: 430, Mismatches: 16, Indels: 45
0.88 0.03 0.09
Matches are distributed among these distances:
119 93 0.22
120 5 0.01
121 81 0.19
122 1 0.00
123 3 0.01
124 5 0.01
125 15 0.03
126 4 0.01
127 5 0.01
128 14 0.03
129 19 0.04
130 5 0.01
131 167 0.39
132 2 0.00
133 7 0.02
134 4 0.01
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (128 bp):
TAATGATTTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAATATTTAATGATTTAATA
ATAATTACTTTAATGATTTAATGATTTAATGATTTAAATTTAATGATTTAATAATAATTACTT
Found at i:118156 original size:23 final size:22
Alignment explanation
Indices: 117741--118369 Score: 238
Period size: 23 Copynumber: 28.9 Consensus size: 22
117731 TAATTATTTA
*
117741 ACTTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAAT-TTAATT
*
117764 ACTTTAATGATTTAACTTTAATG
1 ACTTTAATGATTTAA-TTTAATT
*
117787 A-TTTAAT-A-ATAATTTAA-T
1 ACTTTAATGATTTAATTTAATT
*
117805 --TTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAAT-TTAATT
*
117826 ACTTTAATGATTTAATTTTAATG
1 ACTTTAATGATTTAA-TTTAATT
*
117849 A-TTTAATGATTTAACTTTAATG
1 ACTTTAATGATTTAA-TTTAATT
* * *
117871 A-TTTAATAATAATTACTTTAATG
1 ACTTTAATGAT--TTAATTTAATT
* *
117894 A-TTTAAT--TTTAA-TGATTT
1 ACTTTAATGATTTAATTTAATT
* * * * *
117912 AATAATAATTACTTTAA-TGATTT
1 ACT-TTAATGA-TTTAATTTAATT
*
117935 AACTTTAATGATTTAATAATAATT
1 -ACTTTAATGATTTAAT-TTAATT
* *
117959 ACTTTAATGATTTAA-TGATTT
1 ACTTTAATGATTTAATTTAATT
*
117980 AACTTTAATGATTTAATAATAATT
1 -ACTTTAATGATTTAAT-TTAATT
*
118004 ACTTTAATGATTTAACTTTAATG
1 ACTTTAATGATTTAA-TTTAATT
* * *
118027 A-TTTAATAATAATTACTTTAATG
1 ACTTTAATGAT--TTAATTTAATT
* *
118050 A-TTTAATGATTTAA-TGATTT
1 ACTTTAATGATTTAATTTAATT
* * * *
118070 A--ATAAT-AATTACTTTAATG
1 ACTTTAATGATTTAATTTAATT
118089 A-TTTAATGATTTAA--T-A--
1 ACTTTAATGATTTAATTTAATT
* *
118105 A-TTTAATGATTTAA-TGATTT
1 ACTTTAATGATTTAATTTAATT
* * * * *
118125 AATAATAATTACTTTAA-TGATTT
1 ACT-TTAATGA-TTTAATTTAATT
*
118148 AACTTTAATGATTTAATAATAATT
1 -ACTTTAATGATTTAAT-TTAATT
*
118172 ACTTTAATGATTTAATGATTTAATG
1 ACTTTAATGATTT-A--ATTTAATT
*
118197 A-TTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAAT-TTAATT
* *
118219 ATTTTAATGATTTAATGATTTAATG
1 ACTTTAATGATTT-A--ATTTAATT
*
118244 A-TTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAAT-TTAATT
118266 ACTTTAATGATTTAATTTTAA-T
1 ACTTTAATGATTTAA-TTTAATT
* * *
118288 AATTTAAT-A-ATAA-TTACTT
1 ACTTTAATGATTTAATTTAATT
* *
118307 AATTTTAATGATTTAATTTTAATG
1 -ACTTTAATGATTTAA-TTTAATT
* *
118331 A-TTTAAT-A-ATAA-TTACTT
1 ACTTTAATGATTTAATTTAATT
118349 GACTTTAATGATTTATATTTA
1 -ACTTTAATGATTTA-ATTTA
118370 CTGATATAAT
Statistics
Matches: 470, Mismatches: 76, Indels: 119
0.71 0.11 0.18
Matches are distributed among these distances:
16 14 0.03
17 6 0.01
18 17 0.04
19 24 0.05
20 38 0.08
21 22 0.05
22 102 0.22
23 179 0.38
24 54 0.11
25 10 0.02
26 4 0.01
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (22 bp):
ACTTTAATGATTTAATTTAATT
Found at i:118369 original size:14 final size:13
Alignment explanation
Indices: 117661--118379 Score: 354
Period size: 14 Copynumber: 53.9 Consensus size: 13
117651 TATTTAATAA
*
117661 TAATTATTTAAATT
1 TAATGATTT-AATT
*
117675 TAATTATTTAACTT
1 TAATGATTTAA-TT
*
117689 TAATGATTTAATAA
1 TAATGATTTAAT-T
*
117703 TAATTATTTAACTT
1 TAATGATTTAA-TT
*
117717 TAATGATTTAATAA
1 TAATGATTTAAT-T
*
117731 TAATTATTTAACTT
1 TAATGATTTAA-TT
117745 TAATGATTTAA--
1 TAATGATTTAATT
* *
117756 TAAT-AATTACTT
1 TAATGATTTAATT
117768 TAATGATTTAACTT
1 TAATGATTTAA-TT
117782 TAATGATTTAA--
1 TAATGATTTAATT
*
117793 TAATAATTTAATTT
1 TAATGATTTAA-TT
117807 TAATGATTTAA--
1 TAATGATTTAATT
* *
117818 TAAT-AATTACTT
1 TAATGATTTAATT
117830 TAATGATTTAATTT
1 TAATGATTTAA-TT
117844 TAATG-----ATT
1 TAATGATTTAATT
117852 TAATGATTTAACTT
1 TAATGATTTAA-TT
117866 TAATGATTTAA--
1 TAATGATTTAATT
* *
117877 TAAT-AATTACTT
1 TAATGATTTAATT
117889 TAATGATTTAATTT
1 TAATGATTTAA-TT
117903 TAATGATTTAA--
1 TAATGATTTAATT
* *
117914 TAAT-AATTACTT
1 TAATGATTTAATT
117926 TAATGATTTAACTT
1 TAATGATTTAA-TT
*
117940 TAATGATTTAATAA
1 TAATGATTTAAT-T
*
117954 TAATTACTTTAATGATT
1 TAATGA-TTT-A--ATT
117971 TAATGATTTAACTT
1 TAATGATTTAA-TT
117985 TAATGATTTAA--
1 TAATGATTTAATT
* *
117996 TAAT-AATTACTT
1 TAATGATTTAATT
118008 TAATGATTTAACTT
1 TAATGATTTAA-TT
118022 TAATGATTTAA--
1 TAATGATTTAATT
* *
118033 TAAT-AATTACTT
1 TAATGATTTAATT
118045 TAATGATTTAATGATT
1 TAATGATTT-A--ATT
118061 TAATGATTTAA--
1 TAATGATTTAATT
* *
118072 TAAT-AATTACTT
1 TAATGATTTAATT
118084 TAATGATTTAATGATT
1 TAATGATTT-A--ATT
*
118100 TAATAATTTAATGATT
1 TAATGATTT-A--ATT
118116 TAATGATTTAA--
1 TAATGATTTAATT
* *
118127 TAAT-AATTACTT
1 TAATGATTTAATT
118139 TAATGATTTAACTT
1 TAATGATTTAA-TT
*
118153 TAATGATTTAATAA
1 TAATGATTTAAT-T
*
118167 TAATTACTTTAATGATT
1 TAATGA-TTT-A--ATT
118184 TAATGATTTAATGATT
1 TAATGATTT-A--ATT
*
118200 TAATGATTTAATAA
1 TAATGATTTAAT-T
*
118214 TAATTATTTTAATGATT
1 TAATGA-TTT-A--ATT
118231 TAATGATTTAATGATT
1 TAATGATTT-A--ATT
118247 TAATGATTTAA--
1 TAATGATTTAATT
* *
118258 TAAT-AATTACTT
1 TAATGATTTAATT
118270 TAATGATTTAATTT
1 TAATGATTTAA-TT
* *
118284 TAATAATTTAATAA
1 TAATGATTTAAT-T
* *
118298 TAATTACTTAATTT
1 TAATGATTTAA-TT
118312 TAATGATTTAATTT
1 TAATGATTTAA-TT
*
118326 TAATGATTTAATAA
1 TAATGATTTAAT-T
* * *
118340 TAATTACTTGACTT
1 TAATGA-TTTAATT
118354 TAATGATTTATATT
1 TAATGATTTA-ATT
* *
118368 TACTGATATAAT
1 TAATGATTTAAT
118380 AATAGTAAAT
Statistics
Matches: 552, Mismatches: 78, Indels: 151
0.71 0.10 0.19
Matches are distributed among these distances:
8 7 0.01
9 1 0.00
10 36 0.07
11 46 0.08
12 36 0.07
13 54 0.10
14 250 0.45
15 21 0.04
16 80 0.14
17 15 0.03
18 6 0.01
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (13 bp):
TAATGATTTAATT
Found at i:118414 original size:131 final size:128
Alignment explanation
Indices: 117793--118382 Score: 705
Period size: 131 Copynumber: 4.6 Consensus size: 128
117783 AATGATTTAA
* *
117793 TAATAATTTAAT-TTTAATGATTTAATAATAATTACTTTAATGATTTAAT--TTTAATGATTTAA
1 TAATGATTTAATATTTAATGATTTAATAATAATTAC-TT-ATGATTTAATGATTTAATAATTTAA
117855 TGATTTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAA
64 TGATTTAA---T-A--ATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAA
117920 TTACTT
123 TTACTT
* *
117926 TAATGATTTAA-CTTTAATGATTTAATAATAATTAC------TTTAATGATTTAATGATTTAA--
1 TAATGATTTAATATTTAATGATTTAATAATAATTACTTATGATTTAATGATTTAATAATTTAATG
* * *
117982 CTTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAATAATAATTACTT
66 ATTTAATAATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTACTT
118045 TAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATAATTTA
1 TAATGATTTAAT-ATTTAATGATTTAATAATAATTAC-TT-ATGATTTAATGATTTAATAATTTA
* *
118110 ATGATTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAATAATAATTACT
63 ATGATTTAATAATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTACT
118175 T
128 T
* * *
118176 TAATGATTTAATGATTTAATGATTTAATGATTTAATAATAATTAT--TTTAATGATTTAATGATT
1 TAATGATTTAAT-ATTTAATGATTTAAT-A-ATAAT--TACTTATGATTTAATGATTTAATAATT
* *
118239 TAATGATTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATAATTTAATAATAATTA
61 TAATGATTTAATAATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTA
118304 CTTAATTT
126 C-----TT
*
118312 TAATGATTTAAT-TTTAATGATTTAATAATAATTAC-T-TGACTTTAATGATTT-AT-ATTTACT
1 TAATGATTTAATATTTAATGATTTAATAATAATTACTTATGA-TTTAATGATTTAATAATTTAAT
*
118372 GATATAATAAT
65 GATTTAATAAT
118383 AGTAAATATA
Statistics
Matches: 413, Mismatches: 17, Indels: 58
0.85 0.03 0.12
Matches are distributed among these distances:
119 65 0.16
121 23 0.06
122 1 0.00
125 11 0.03
127 13 0.03
128 1 0.00
129 36 0.09
130 4 0.01
131 182 0.44
132 5 0.01
133 40 0.10
134 16 0.04
135 2 0.00
136 14 0.03
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (128 bp):
TAATGATTTAATATTTAATGATTTAATAATAATTACTTATGATTTAATGATTTAATAATTTAATG
ATTTAATAATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTACTT
Found at i:120879 original size:172 final size:173
Alignment explanation
Indices: 120584--120942 Score: 562
Period size: 172 Copynumber: 2.1 Consensus size: 173
120574 ACATCAATAT
* *
120584 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
120649 TATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAAC
66 TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
* * *
120714 TTTTTATAATTTACTCTAATTTCTTAAATT-CTTCAAATTTTGC
131 TTTTAATAATTTACTCTAATTCCTTAAATTCCTT-AAATTTTAC
* *
120757 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAAGTTAGCAATTTAATC-CATAAAT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* * *
120821 TT-TAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAGCAA
65 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAA
*
120885 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
130 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTTAAATTTTAC
*
120929 AAAACGGTCCCTAA
1 AAAACGATCCCTAA
120943 AACTTTACAA
Statistics
Matches: 171, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
172 108 0.63
173 63 0.37
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (173 bp):
AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
TTTTAATAATTTACTCTAATTCCTTAAATTCCTTAAATTTTAC
Found at i:121484 original size:22 final size:22
Alignment explanation
Indices: 121456--121509 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
121446 AGGACCCAGG
121456 ACCCGTGATTTCTCCTTGCAGA
1 ACCCGTGATTTCTCCTTGCAGA
* *
121478 ACCCGTGCTCTCTCCTTGCAGA
1 ACCCGTGATTTCTCCTTGCAGA
121500 ACCCGTGATT
1 ACCCGTGATT
121510 CTCACGTCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.17, C:0.35, G:0.19, T:0.30
Consensus pattern (22 bp):
ACCCGTGATTTCTCCTTGCAGA
Found at i:122488 original size:2 final size:2
Alignment explanation
Indices: 122483--122510 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
122473 TTCCCTTCAA
122483 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
122511 GAACAGTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:125212 original size:17 final size:17
Alignment explanation
Indices: 125187--125219 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
125177 GAAACCTTAG
*
125187 CTTTTCAACAAAAATAT
1 CTTTACAACAAAAATAT
125204 CTTTACAACAAAAATA
1 CTTTACAACAAAAATA
125220 CGCTACTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (17 bp):
CTTTACAACAAAAATAT
Found at i:125958 original size:60 final size:60
Alignment explanation
Indices: 125865--125986 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
125855 TAATGGACTG
125865 ATTAATTAATATGTTTGATTTGATCCATTAAATACTTTTATGGAAATGTAATAATAATTT
1 ATTAATTAATATGTTTGATTTGATCCATTAAATACTTTTATGGAAATGTAATAATAATTT
125925 ATTAATTAATATGTTTGATTTGATCCATTAAATACTTTTATGGAAATGTAATAATAATTT
1 ATTAATTAATATGTTTGATTTGATCCATTAAATACTTTTATGGAAATGTAATAATAATTT
125985 AT
1 AT
125987 AAAATATTAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.47
Consensus pattern (60 bp):
ATTAATTAATATGTTTGATTTGATCCATTAAATACTTTTATGGAAATGTAATAATAATTT
Found at i:126074 original size:12 final size:13
Alignment explanation
Indices: 126049--126073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
126039 TTGTAATAAT
126049 TATGATTAAAAAA
1 TATGATTAAAAAA
126062 TATGATTAAAAA
1 TATGATTAAAAA
126074 TTCAATAATA
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (13 bp):
TATGATTAAAAAA
Found at i:131555 original size:2 final size:2
Alignment explanation
Indices: 131548--131578 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
131538 GTACATTAAG
131548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
131579 AATAATAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.