Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 6 of 160
Found at i:1569902 original size:16 final size:16
Alignment explanation
Indices: 1569877--1569916 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1569867 TGATAAACTA
*
1569877 ATGATAATGATGATTT
1 ATGATGATGATGATTT
1569893 ATGATGATGATGATTT
1 ATGATGATGATGATTT
*
1569909 ACGATGAT
1 ATGATGAT
1569917 TTTTAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.40
Consensus pattern (16 bp):
ATGATGATGATGATTT
Found at i:1574677 original size:20 final size:20
Alignment explanation
Indices: 1574652--1574690 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1574642 TTCTAAATTG
1574652 GTAATGAAAACATCGACAGT
1 GTAATGAAAACATCGACAGT
1574672 GTAATGAAAACATCGACAG
1 GTAATGAAAACATCGACAG
1574691 GGGGGAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (20 bp):
GTAATGAAAACATCGACAGT
Found at i:1583905 original size:12 final size:12
Alignment explanation
Indices: 1583883--1583916 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1583873 TCTTTTTTTT
*
1583883 GAGAGAAAAGAA
1 GAGAAAAAAGAA
*
1583895 GGGAAAAAAGAA
1 GAGAAAAAAGAA
1583907 GAGAAAAAAG
1 GAGAAAAAAG
1583917 TGCAATATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (12 bp):
GAGAAAAAAGAA
Found at i:1604692 original size:30 final size:29
Alignment explanation
Indices: 1604641--1604707 Score: 107
Period size: 30 Copynumber: 2.3 Consensus size: 29
1604631 TAGAAATATT
*
1604641 TATTTATACAAATTAGTAGTATAAAGATA
1 TATTTGTACAAATTAGTAGTATAAAGATA
*
1604670 TATTTGTACAAGTTAGGTAGTATAAAGATA
1 TATTTGTACAAATTA-GTAGTATAAAGATA
1604700 TATTTGTA
1 TATTTGTA
1604708 TATAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 13 0.37
30 22 0.63
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (29 bp):
TATTTGTACAAATTAGTAGTATAAAGATA
Found at i:1607274 original size:11 final size:11
Alignment explanation
Indices: 1607258--1607287 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1607248 CAGCGATCCT
*
1607258 TAAATTTTGAG
1 TAAATTTCGAG
1607269 TAAATTTCGAG
1 TAAATTTCGAG
1607280 TAAATTTC
1 TAAATTTC
1607288 TATTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (11 bp):
TAAATTTCGAG
Found at i:1614793 original size:2 final size:2
Alignment explanation
Indices: 1614786--1614810 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1614776 TACAAATCTA
1614786 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 A
1614811 GTTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1622312 original size:13 final size:13
Alignment explanation
Indices: 1622294--1622319 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1622284 ATTATTTGAC
1622294 TTGACTGTCAGCA
1 TTGACTGTCAGCA
1622307 TTGACTGTCAGCA
1 TTGACTGTCAGCA
1622320 ACACCAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TTGACTGTCAGCA
Found at i:1623253 original size:42 final size:42
Alignment explanation
Indices: 1623199--1623284 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 42
1623189 AATACATAGT
* * *
1623199 TATTATATATAGGATTCCAGA-CGAGAGAATTAGTTAAAGTTA
1 TATTATATATAGGATTCCAGATC-AGAGAATCAGTCAAAATTA
1623241 TATTATATATAGGATTCCAGATCAGAGAATCAGTCAAAATTA
1 TATTATATATAGGATTCCAGATCAGAGAATCAGTCAAAATTA
1623283 TA
1 TA
1623285 CTGCAGAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 39 0.98
43 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (42 bp):
TATTATATATAGGATTCCAGATCAGAGAATCAGTCAAAATTA
Found at i:1631853 original size:58 final size:58
Alignment explanation
Indices: 1631778--1631900 Score: 167
Period size: 58 Copynumber: 2.1 Consensus size: 58
1631768 CCAAGAATTT
* *
1631778 TTTGTTTGATTTCAAAAACCAAAATATTTTACC-TACTGTTGAAACTAAGAAATTTTTG
1 TTTGTTTGATTTCAAAAACCAAAATACTTT-CCTTACTGTTGAAACCAAGAAATTTTTG
* * * * *
1631836 TTTGTTTGATTTCAAAAACCTAAATCCTTTCCTTGCTGTTGGAACCAATAAATTTTTG
1 TTTGTTTGATTTCAAAAACCAAAATACTTTCCTTACTGTTGAAACCAAGAAATTTTTG
1631894 TTTGTTT
1 TTTGTTT
1631901 TCAAACATTC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 2 0.04
58 55 0.96
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (58 bp):
TTTGTTTGATTTCAAAAACCAAAATACTTTCCTTACTGTTGAAACCAAGAAATTTTTG
Found at i:1632791 original size:3 final size:3
Alignment explanation
Indices: 1632783--1632829 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1632773 TAATGAGTAA
1632783 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1632830 AGATAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1633883 original size:15 final size:15
Alignment explanation
Indices: 1633863--1633893 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1633853 AAACTTTCTC
*
1633863 TTTTTTTATCTTTTT
1 TTTTTTTACCTTTTT
1633878 TTTTTTTACCTTTTT
1 TTTTTTTACCTTTTT
1633893 T
1 T
1633894 GAGAAAAAAG
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:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTACCTTTTT
Found at i:1634845 original size:3 final size:3
Alignment explanation
Indices: 1634831--1634867 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1634821 ATCATTTAAT
1634831 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1634868 TTATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1634872 original size:3 final size:3
Alignment explanation
Indices: 1634866--1634895 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1634856 ATAATAATAA
1634866 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1634896 CATAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1635139 original size:5 final size:5
Alignment explanation
Indices: 1635131--1635155 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1635121 ATCGATGCTT
1635131 GCATG GCATG GCATG GCATG GCATG
1 GCATG GCATG GCATG GCATG GCATG
1635156 ATTAATTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (5 bp):
GCATG
Found at i:1635582 original size:2 final size:2
Alignment explanation
Indices: 1635575--1635626 Score: 63
Period size: 2 Copynumber: 26.5 Consensus size: 2
1635565 ATCCCTCCTT
*
1635575 TA TA TA TA TA TA TA TA TA TA T- TA -A TA TC TCA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
*
1635616 TA TA TG TA TA T
1 TA TA TA TA TA T
1635627 GAGGTATCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.93
3 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1636192 original size:2 final size:2
Alignment explanation
Indices: 1636179--1636226 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
1636169 TGATCCTTTC
* *
1636179 AT AT AT AC AT AT AT AT AT AT AC AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1636220 AT AT AT A
1 AT AT AT A
1636227 AATAGAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1636633 original size:3 final size:3
Alignment explanation
Indices: 1636625--1636652 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1636615 TTCATTTCAT
1636625 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1636653 TATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1636657 original size:3 final size:3
Alignment explanation
Indices: 1636651--1636675 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1636641 AATAATAATA
1636651 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1636676 AAGATAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1639167 original size:29 final size:29
Alignment explanation
Indices: 1639089--1639167 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
1639079 TATAATCTAA
* *
1639089 ATATTATTGTATTATAATTTATATTT-ATAT
1 ATATAATTGTATTAAAATTT-TATTTAAT-T
* *
1639119 ATATAATTGGA-TATATATTTTATTTAATT
1 ATATAATTGTATTA-AAATTTTATTTAATT
*
1639148 ATATAATTTTATTAAAATTT
1 ATATAATTGTATTAAAATTT
1639168 ATTATTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
29 22 0.56
30 17 0.44
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (29 bp):
ATATAATTGTATTAAAATTTTATTTAATT
Found at i:1639174 original size:18 final size:18
Alignment explanation
Indices: 1639089--1639175 Score: 54
Period size: 18 Copynumber: 4.6 Consensus size: 18
1639079 TATAATCTAA
*
1639089 ATATTATTGTATTATAATT
1 ATATTATTTTATTA-AATT
1639108 -TA-TATTTATATATATAATT
1 ATATTATTT-TAT-TA-AATT
*
1639127 GGATATATATTTTATTTAATT
1 --ATAT-TATTTTATTAAATT
*
1639148 ATATAATTTTATTAAAATT
1 ATATTATTTTATT-AAATT
1639167 -TATTATTTT
1 ATATTATTTT
1639176 TATATTAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
17 4 0.07
18 21 0.38
19 15 0.27
21 4 0.07
22 3 0.05
23 3 0.05
24 5 0.09
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
ATATTATTTTATTAAATT
Found at i:1639188 original size:19 final size:18
Alignment explanation
Indices: 1639135--1639189 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
1639125 TTGGATATAT
1639135 ATTTTATTT-AATTATATA
1 ATTTTATTTAAATTAT-TA
*
1639153 ATTTTATTAAAATTTATTA
1 ATTTTATTTAAA-TTATTA
*
1639172 TTTTTATATTAAATTATT
1 ATTTTAT-TTAAATTATT
1639190 GTATCCGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 8 0.26
19 15 0.48
20 8 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTATTTAAATTATTA
Found at i:1641167 original size:14 final size:13
Alignment explanation
Indices: 1641122--1641164 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 13
1641112 ATTTTAAAAA
1641122 TAAATATAATTAAT
1 TAAATA-AATTAAT
*
1641136 TCAATAAAATTTAAT
1 TAAAT-AAA-TTAAT
1641151 TAAATAAATTAAT
1 TAAATAAATTAAT
1641164 T
1 T
1641165 TAAGAACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 6 0.24
14 9 0.36
15 10 0.40
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (13 bp):
TAAATAAATTAAT
Found at i:1642036 original size:11 final size:11
Alignment explanation
Indices: 1642020--1642059 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1642010 TTAACATATG
1642020 ATATAAAAATA
1 ATATAAAAATA
*
1642031 ATATAAATAAAA
1 ATATAAA-AATA
*
1642043 ATATTAAAATA
1 ATATAAAAATA
1642054 ATATAA
1 ATATAA
1642060 TTTAAAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:1652596 original size:112 final size:112
Alignment explanation
Indices: 1652399--1652623 Score: 387
Period size: 112 Copynumber: 2.0 Consensus size: 112
1652389 CTAACTTGGG
* *
1652399 AGAAAATAGGCCCATAACTCTTCATAATGGCTCAATTTGTGCTCCTTGGTATACCAAATAAATTT
1 AGAAAATAGGCCCATAACTCTTCAGAATGGCCCAATTTGTGCTCCTTGGTATACCAAATAAATTT
* *
1652464 GAGCTATTATAAATATTTGATAATTTTATTTTATTTTTAAAATTTTA
66 GAGCAACTATAAATATTTGATAATTTTATTTTATTTTTAAAATTTTA
* *
1652511 AGAAAATAGGCCCATAACTCTTCAGAATGGCCCAATTTGTTCTCCTTGGTATATCAAATAAATTT
1 AGAAAATAGGCCCATAACTCTTCAGAATGGCCCAATTTGTGCTCCTTGGTATACCAAATAAATTT
*
1652576 GAGCAACTATAAATATTTGATAATTTTATTTTATTTTTTAAATTTTA
66 GAGCAACTATAAATATTTGATAATTTTATTTTATTTTTAAAATTTTA
1652623 A
1 A
1652624 TCTATCCCTA
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 106 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (112 bp):
AGAAAATAGGCCCATAACTCTTCAGAATGGCCCAATTTGTGCTCCTTGGTATACCAAATAAATTT
GAGCAACTATAAATATTTGATAATTTTATTTTATTTTTAAAATTTTA
Found at i:1652650 original size:15 final size:17
Alignment explanation
Indices: 1652613--1652653 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1652603 ATTTTATTTT
1652613 TTAAATTTTAATCTATCC
1 TTAAATTTT-ATCTATCC
*
1652631 CTAAATTTT-TC-ATCC
1 TTAAATTTTATCTATCC
1652646 TTAAATTT
1 TTAAATTT
1652654 ATTTAGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 11 0.52
16 2 0.10
18 8 0.38
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAATTTTATCTATCC
Found at i:1654764 original size:30 final size:29
Alignment explanation
Indices: 1654716--1654775 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 29
1654706 AAAATGTCAT
*
1654716 TGATATATATATGGTAGCAACACTTAGGA
1 TGATATATATATGGTAGCAAAACTTAGGA
1654745 TGATATATAT-TCCGGTAGCAAAACTTAGGA
1 TGATATATATAT--GGTAGCAAAACTTAGGA
1654775 T
1 T
1654776 TGTGGAACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 1 0.04
29 10 0.36
30 17 0.61
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (29 bp):
TGATATATATATGGTAGCAAAACTTAGGA
Found at i:1657873 original size:74 final size:74
Alignment explanation
Indices: 1657752--1657901 Score: 300
Period size: 74 Copynumber: 2.0 Consensus size: 74
1657742 TCCTTTATAG
1657752 TGGGAATACAACCTGTGACTTCTTTCAGTTAAACATTACCTTTTTATCAGTCATTAATATGAGAT
1 TGGGAATACAACCTGTGACTTCTTTCAGTTAAACATTACCTTTTTATCAGTCATTAATATGAGAT
1657817 GGTGACTAT
66 GGTGACTAT
1657826 TGGGAATACAACCTGTGACTTCTTTCAGTTAAACATTACCTTTTTATCAGTCATTAATATGAGAT
1 TGGGAATACAACCTGTGACTTCTTTCAGTTAAACATTACCTTTTTATCAGTCATTAATATGAGAT
1657891 GGTGACTAT
66 GGTGACTAT
1657900 TG
1 TG
1657902 CATTGCATGT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (74 bp):
TGGGAATACAACCTGTGACTTCTTTCAGTTAAACATTACCTTTTTATCAGTCATTAATATGAGAT
GGTGACTAT
Found at i:1674336 original size:15 final size:15
Alignment explanation
Indices: 1674316--1674350 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1674306 ATACTTATAG
*
1674316 TAATATTTTATTTCT
1 TAATATTTTATCTCT
1674331 TAATATTTTATCTCT
1 TAATATTTTATCTCT
1674346 TAATA
1 TAATA
1674351 CAAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (15 bp):
TAATATTTTATCTCT
Found at i:1675253 original size:20 final size:21
Alignment explanation
Indices: 1675217--1675258 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1675207 TAACAAAATT
*
1675217 TTTTAATTTATCAATTT-TAA
1 TTTTAATTTAACAATTTCTAA
*
1675237 TTTTAATTTAACTATTTCTAA
1 TTTTAATTTAACAATTTCTAA
1675258 T
1 T
1675259 AAAAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAATTTAACAATTTCTAA
Found at i:1679381 original size:25 final size:25
Alignment explanation
Indices: 1679347--1679396 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1679337 GTTATTTTAG
1679347 GACAAAAACGTGTAATAAATTGTCT
1 GACAAAAACGTGTAATAAATTGTCT
1679372 GACAAAAACGTGTAATAAATTGTCT
1 GACAAAAACGTGTAATAAATTGTCT
1679397 TAGAATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (25 bp):
GACAAAAACGTGTAATAAATTGTCT
Found at i:1682013 original size:20 final size:21
Alignment explanation
Indices: 1681975--1682014 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1681965 CAATGAAGTA
*
1681975 CAATTAAATTTTAATTATTAT
1 CAATTAAATTTTAAATATTAT
1681996 CAATTAAA-TTTAAATATTA
1 CAATTAAATTTTAAATATTA
1682015 ATTTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
CAATTAAATTTTAAATATTAT
Found at i:1682075 original size:22 final size:22
Alignment explanation
Indices: 1682058--1682103 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1682048 ACTATAAATT
1682058 TTTTTAATCATAATTATAATAA
1 TTTTTAATCATAATTATAATAA
*
1682080 TTTTTAATCATAATTACAATAA
1 TTTTTAATCATAATTATAATAA
1682102 TT
1 TT
1682104 ATTATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTTAATCATAATTATAATAA
Found at i:1683115 original size:3 final size:3
Alignment explanation
Indices: 1683107--1683131 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1683097 TTTATACTCA
1683107 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1683132 GCTAATTCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1693638 original size:17 final size:16
Alignment explanation
Indices: 1693616--1693647 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
1693606 GTTTGTCCGG
1693616 TTTTTTGTTTCTTTTTT
1 TTTTTTG-TTCTTTTTT
1693633 TTTTTTGTTCTTTTT
1 TTTTTTGTTCTTTTT
1693648 CTTCTTGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (16 bp):
TTTTTTGTTCTTTTTT
Found at i:1699116 original size:16 final size:16
Alignment explanation
Indices: 1699095--1699125 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1699085 CAAAAATGCT
1699095 TTTTTTTTTGTTTTTG
1 TTTTTTTTTGTTTTTG
1699111 TTTTTTTTTGTTTTT
1 TTTTTTTTTGTTTTT
1699126 AATAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (16 bp):
TTTTTTTTTGTTTTTG
Found at i:1699923 original size:20 final size:21
Alignment explanation
Indices: 1699886--1699926 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1699876 TTTTGATAAA
1699886 CTTTAATTTAATAATGAATTT
1 CTTTAATTTAATAATGAATTT
**
1699907 CTTT-ATTTAATTTTGAATTT
1 CTTTAATTTAATAATGAATTT
1699927 TAATTTGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
CTTTAATTTAATAATGAATTT
Found at i:1703281 original size:20 final size:20
Alignment explanation
Indices: 1703240--1703282 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1703230 TAAATTTTAA
* * *
1703240 ATCGTATTATTTTTATATTT
1 ATCGTATTATATTTAAAATT
1703260 ATCGTATTATATTTAAAATT
1 ATCGTATTATATTTAAAATT
1703280 ATC
1 ATC
1703283 ACGTTTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATCGTATTATATTTAAAATT
Found at i:1729573 original size:17 final size:17
Alignment explanation
Indices: 1729526--1729574 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1729516 TTTTTTATTT
*
1729526 TATTTTAATATTA-TATT
1 TATTTTAA-ATTATTATA
* *
1729543 TATATTATATTATTATA
1 TATTTTAAATTATTATA
1729560 TATTTTAAATTATTA
1 TATTTTAAATTATTA
1729575 AATTAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTTAAATTATTATA
Found at i:1742280 original size:22 final size:21
Alignment explanation
Indices: 1742255--1742302 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1742245 AAAGAATTAT
1742255 TTAATTACAAAT-TCAATTCAAA
1 TTAATT-CAAATATC-ATTCAAA
*
1742277 TTAAATTTAAATATCATTCAAA
1 TT-AATTCAAATATCATTCAAA
1742299 TTAA
1 TTAA
1742303 ATTATTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 2 0.09
22 15 0.65
23 6 0.26
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAATTCAAATATCATTCAAA
Found at i:1742433 original size:32 final size:31
Alignment explanation
Indices: 1742397--1742462 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
1742387 AATTAATCCG
*
1742397 ATTAATTCAATT-ATTAATTTTAAAAATAATAA
1 ATTAATTCAATTAATCAA-TTTAAAAA-AATAA
* *
1742429 ATTAATTTAATTAATCAATTTAAAAAAATTA
1 ATTAATTCAATTAATCAATTTAAAAAAATAA
1742460 ATT
1 ATT
1742463 GTAACCAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 7 0.23
32 19 0.63
33 4 0.13
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
ATTAATTCAATTAATCAATTTAAAAAAATAA
Found at i:1751356 original size:13 final size:13
Alignment explanation
Indices: 1751336--1751378 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
1751326 TTGATAATTT
1751336 AAAATATTATATA
1 AAAATATTATATA
*
1751349 ATAATATTATATA
1 AAAATATTATATA
*
1751362 AAAATAATAT-TA
1 AAAATATTATATA
1751374 AAAAT
1 AAAAT
1751379 TTTAAAGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATATTATATA
Found at i:1756320 original size:2 final size:2
Alignment explanation
Indices: 1756313--1756339 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1756303 CAGAACAAAC
1756313 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1756340 CAAACACGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1757048 original size:21 final size:22
Alignment explanation
Indices: 1757019--1757065 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
1757009 CGTATTTAAT
1757019 ATAAGATTATAATA-AAATAAA
1 ATAAGATTATAATATAAATAAA
* *
1757040 ATAATATTATATTATAAATAAA
1 ATAAGATTATAATATAAATAAA
1757062 ATAA
1 ATAA
1757066 AATAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
ATAAGATTATAATATAAATAAA
Found at i:1757067 original size:27 final size:26
Alignment explanation
Indices: 1757015--1757081 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 26
1757005 AGATCGTATT
*
1757015 TAATATAAGATTATAATAAAATAAAA
1 TAATATAATATTATAATAAAATAAAA
*
1757041 TAATATTATATTATAAATAAAATAAAA
1 TAATATAATATTAT-AATAAAATAAAA
*
1757068 TAAAATAATATTAT
1 TAATATAATATTAT
1757082 TTTATCTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 12 0.33
27 24 0.67
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (26 bp):
TAATATAATATTATAATAAAATAAAA
Found at i:1757168 original size:17 final size:18
Alignment explanation
Indices: 1757148--1757185 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1757138 AAAATTATTT
*
1757148 TTTAAA-AATTTATATAA
1 TTTAAATAATTAATATAA
*
1757165 TTTAAATTATTAATATAA
1 TTTAAATAATTAATATAA
1757183 TTT
1 TTT
1757186 TTAAGAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATAATTAATATAA
Found at i:1763063 original size:16 final size:15
Alignment explanation
Indices: 1763035--1763064 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1763025 TATTAATCAA
1763035 TATTATTTATTAATG
1 TATTATTTATTAATG
1763050 TATTATTGTATTAAT
1 TATTATT-TATTAAT
1763065 AATATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TATTATTTATTAATG
Found at i:1763103 original size:15 final size:15
Alignment explanation
Indices: 1763023--1763105 Score: 58
Period size: 18 Copynumber: 4.9 Consensus size: 15
1763013 TGAGCACATT
1763023 TTTATTAATCAATATTA
1 TTTATTAA--AATATTA
**
1763040 TTTATTAATGTATTA
1 TTTATTAAAATATTA
1763055 TTGTATTAATAATATATTA
1 TT-TATT-A-AA-ATATTA
*
1763074 TCTATTCATATAATATTA
1 TTTATT-A-A-AATATTA
1763092 TTTATTAAAATATT
1 TTTATTAAAATATT
1763106 GTAATATAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
15 13 0.24
16 5 0.09
17 10 0.19
18 19 0.35
19 7 0.13
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTATTAAAATATTA
Found at i:1763113 original size:28 final size:23
Alignment explanation
Indices: 1763081--1763148 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 23
1763071 TTATCTATTC
1763081 ATATAATATTATTTATTAAAATATTGTA
1 ATATAATATTATTTATT---ATA-TG-A
1763109 ATATAATATTATTTATT-TATGA
1 ATATAATATTATTTATTATATGA
1763131 ATATAATATTATTTATTA
1 ATATAATATTATTTATTA
1763149 GTAAATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
22 18 0.46
23 2 0.05
24 2 0.05
28 17 0.44
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (23 bp):
ATATAATATTATTTATTATATGA
Found at i:1763144 original size:18 final size:17
Alignment explanation
Indices: 1763033--1763146 Score: 60
Period size: 18 Copynumber: 6.7 Consensus size: 17
1763023 TTTATTAATC
*
1763033 AATATTATTTATTA-AT
1 AATATTATTTATAATAT
*
1763049 -GTATTATTGTATTAATA-
1 AATATTATT-TA-TAATAT
* *
1763066 ATATATTATCTATTCATAT
1 A-ATATTATTTA-TAATAT
*
1763085 AATATTATTTAT--TAA
1 AATATTATTTATAATAT
* *
1763100 AATATTGTAATATAATAT
1 AATATTAT-TTATAATAT
*
1763118 TAT-TTATTTATGAATAT
1 AATATTATTTAT-AATAT
1763135 AATATTATTTAT
1 AATATTATTTAT
1763147 TAGTAAATTT
Statistics
Matches: 73, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
15 16 0.22
16 8 0.11
17 13 0.18
18 29 0.40
19 7 0.10
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (17 bp):
AATATTATTTATAATAT
Found at i:1763147 original size:50 final size:50
Alignment explanation
Indices: 1763033--1763148 Score: 137
Period size: 50 Copynumber: 2.3 Consensus size: 50
1763023 TTTATTAATC
* **
1763033 AATATTATTTATTAATGTATTATTGTATTAATAATATATTATCTATTCATAT
1 AATATTATTTATTAA--TAATATTGTATTAATAATATATTATCTATGAATAT
* *
1763085 AATATTATTTATTAA-AATATTGTAAT-ATAATATTATTTATTTATGAATAT
1 AATATTATTTATTAATAATATTGTATTAATAATA-TA-TTATCTATGAATAT
1763135 AATATTATTTATTA
1 AATATTATTTATTA
1763149 GTAAATTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
48 6 0.11
49 11 0.19
50 25 0.44
52 15 0.26
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (50 bp):
AATATTATTTATTAATAATATTGTATTAATAATATATTATCTATGAATAT
Found at i:1763350 original size:14 final size:15
Alignment explanation
Indices: 1763323--1763351 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1763313 CTTAAAAATA
1763323 TAAAAATAATTTTTT
1 TAAAAATAATTTTTT
1763338 TAAAAATAATTTTT
1 TAAAAATAATTTTT
1763352 CGTGAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAAAATAATTTTTT
Found at i:1768337 original size:14 final size:15
Alignment explanation
Indices: 1768309--1768338 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1768299 GTTGGAGAAA
1768309 AAGTGGAATAATTAC
1 AAGTGGAATAATTAC
1768324 AAGTGGAA-AATTAC
1 AAGTGGAATAATTAC
1768338 A
1 A
1768339 TCCACTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (15 bp):
AAGTGGAATAATTAC
Found at i:1774888 original size:31 final size:31
Alignment explanation
Indices: 1774847--1774915 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
1774837 TTCTGTAGGG
*
1774847 ACAAGTTAAAAGCAACAGCTTAGACACAAAC
1 ACAAGCTAAAAGCAACAGCTTAGACACAAAC
1774878 ACAAGCTAAAAGCAACAGCTTAGACACAAAC
1 ACAAGCTAAAAGCAACAGCTTAGACACAAAC
1774909 ACAAGCT
1 ACAAGCT
1774916 TGGATGCATG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.51, C:0.25, G:0.13, T:0.12
Consensus pattern (31 bp):
ACAAGCTAAAAGCAACAGCTTAGACACAAAC
Found at i:1781092 original size:18 final size:18
Alignment explanation
Indices: 1781078--1781133 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
1781068 AACTATTTTT
1781078 TATTTTTATTATATTTAA
1 TATTTTTATTATATTTAA
1781096 TATTTTTATTATATTTAA
1 TATTTTTATTATATTTAA
*
1781114 TCTCATTATTATTATATTTA
1 --T-ATTTTTATTATATTTA
1781134 TATCAAACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 18 0.53
20 1 0.03
21 15 0.44
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTTATTATATTTAA
Found at i:1781748 original size:28 final size:29
Alignment explanation
Indices: 1781697--1781760 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
1781687 AAATTCATAA
* *
1781697 ATTTTATTATATTTCTTAGATAAAGTTTTAT
1 ATTTTATTATA-TTCTTAAATAAAATTTT-T
1781728 ATTTTATTATA-T-TTAAATAAAATTTTT
1 ATTTTATTATATTCTTAAATAAAATTTTT
1781755 ATTTTA
1 ATTTTA
1781761 ATTTTACACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 7 0.23
28 12 0.39
29 1 0.03
31 11 0.35
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (29 bp):
ATTTTATTATATTCTTAAATAAAATTTTT
Found at i:1781844 original size:18 final size:19
Alignment explanation
Indices: 1781823--1781863 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1781813 TTATTTTTAA
*
1781823 TTTATATTTAAA-TAATTC
1 TTTATATATAAATTAATTC
*
1781841 TTTA-ATATAAATTAATTT
1 TTTATATATAAATTAATTC
1781859 TTTAT
1 TTTAT
1781864 TCAAAGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATATAAATTAATTC
Found at i:1786565 original size:15 final size:14
Alignment explanation
Indices: 1786545--1786574 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1786535 AAAGTAGGAG
1786545 GAAGAGGAGGGAAGA
1 GAAGAGGA-GGAAGA
1786560 GAAGAGGAGGAAGA
1 GAAGAGGAGGAAGA
1786574 G
1 G
1786575 GGATGAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (14 bp):
GAAGAGGAGGAAGA
Found at i:1803015 original size:13 final size:13
Alignment explanation
Indices: 1802983--1803030 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1802973 ATTAATTCGA
1802983 ATTTTAAATCAATT
1 ATTTTAAAT-AATT
* *
1802997 AATTTATATAATT
1 ATTTTAAATAATT
*
1803010 ATTTTAAAAAATT
1 ATTTTAAATAATT
1803023 ATATTTAA
1 AT-TTTAA
1803031 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTTAAATAATT
Found at i:1803036 original size:27 final size:27
Alignment explanation
Indices: 1802983--1803033 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1802973 ATTAATTCGA
*
1802983 ATTTTAAATCAATTAATTTATATAATT
1 ATTTTAAATAAATTAATTTATATAATT
1803010 ATTTTAAA-AAATTATATTTA-ATAA
1 ATTTTAAATAAATTA-ATTTATATAA
1803034 ATTTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTTAAATAAATTAATTTATATAATT
Found at i:1803598 original size:16 final size:16
Alignment explanation
Indices: 1803577--1803611 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1803567 AATACTAAAA
* *
1803577 TTTTTAATATTTAATT
1 TTTTTAACATTGAATT
1803593 TTTTTAACATTGAATT
1 TTTTTAACATTGAATT
1803609 TTT
1 TTT
1803612 AATTTATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTTTAACATTGAATT
Found at i:1815598 original size:4 final size:4
Alignment explanation
Indices: 1815584--1815613 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1815574 GAGTTGAACG
*
1815584 AATA TATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
1815614 ACGCAGCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:1817492 original size:27 final size:27
Alignment explanation
Indices: 1817440--1817492 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1817430 TCCTTTAGAA
* *
1817440 AGAGGGTTCATGTCGGGTCCGATTGAG
1 AGAGGGTTCATGTCGGGACCCATTGAG
*
1817467 AGAGGGTTCATGTCGGGACCCCTTGA
1 AGAGGGTTCATGTCGGGACCCATTGA
1817493 TAATATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.25
Consensus pattern (27 bp):
AGAGGGTTCATGTCGGGACCCATTGAG
Found at i:1820976 original size:2 final size:2
Alignment explanation
Indices: 1820971--1820997 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1820961 TCTCTCTCTC
1820971 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 T
1820998 TATTTTGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1822886 original size:20 final size:21
Alignment explanation
Indices: 1822851--1822890 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1822841 TTTAAATTAT
1822851 TATTTTTAAAAATTTTTAATC
1 TATTTTTAAAAATTTTTAATC
*
1822872 TATTTTT-AAATTTTTTAAT
1 TATTTTTAAAAATTTTTAAT
1822891 ATTAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTAAAAATTTTTAATC
Found at i:1822938 original size:18 final size:17
Alignment explanation
Indices: 1822892--1822938 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
1822882 TTTTTTAATA
1822892 TTAATTTAATAAAAAAAT
1 TTAATTT-ATAAAAAAAT
* *
1822910 TTAACTCATAAAAAAATT
1 TTAATTTATAAAAAAA-T
1822928 TTAATTTATAA
1 TTAATTTATAA
1822939 TATTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAATTTATAAAAAAAT
Found at i:1823742 original size:16 final size:18
Alignment explanation
Indices: 1823716--1823759 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
1823706 AAAAAATATT
*
1823716 ATATGTTTTATTT-TTTA
1 ATATATTTTATTTATTTA
1823733 AT-TATTTTATTTATTTA
1 ATATATTTTATTTATTTA
*
1823750 TTATATTTTA
1 ATATATTTTA
1823760 AAAAGTATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 9 0.39
17 7 0.30
18 7 0.30
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
ATATATTTTATTTATTTA
Found at i:1832793 original size:18 final size:18
Alignment explanation
Indices: 1832770--1832815 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1832760 AGTTCATAAA
**
1832770 TTTAATTAATTTTTTTAT
1 TTTAATTAATTTAATTAT
1832788 TTTAA-TATATTTAATTAT
1 TTTAATTA-ATTTAATTAT
1832806 TTTAATTAAT
1 TTTAATTAAT
1832816 AAAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTAATTAATTTAATTAT
Found at i:1837245 original size:14 final size:14
Alignment explanation
Indices: 1837237--1837276 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
1837227 AATATTATTT
1837237 TTTAAATATAAATA
1 TTTAAATATAAATA
1837251 TTTAAATATATAATTA
1 TTTAAATATA-AA-TA
*
1837267 TATAAATATA
1 TTTAAATATA
1837277 TTAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 2 0.09
16 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAATATAAATA
Found at i:1837263 original size:16 final size:16
Alignment explanation
Indices: 1837242--1837283 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1837232 TATTTTTTAA
*
1837242 ATATAAATATTTAAAT
1 ATATAAATATATAAAT
*
1837258 ATATAATTATATAAAT
1 ATATAAATATATAAAT
1837274 ATATTAAATA
1 ATA-TAAATA
1837284 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATAAATATATAAAT
Found at i:1837290 original size:25 final size:24
Alignment explanation
Indices: 1837242--1837291 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
1837232 TATTTTTTAA
* *
1837242 ATATAAATATTTAAATATATAATT
1 ATATAAATATTTAAATAAAAAATT
1837266 ATATAAATATATTAAATAAAAAATT
1 ATATAAATAT-TTAAATAAAAAATT
1837291 A
1 A
1837292 ATTTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATAAATATTTAAATAAAAAATT
Found at i:1839739 original size:2 final size:2
Alignment explanation
Indices: 1839734--1839759 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1839724 TTTTCACTTT
1839734 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1839760 GCTAACATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1839875 original size:2 final size:2
Alignment explanation
Indices: 1839868--1839895 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1839858 ATTTCCTTGT
1839868 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1839896 GTTTGGGTTT
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):
TA
Found at i:1840579 original size:40 final size:40
Alignment explanation
Indices: 1840535--1840611 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
1840525 CGTACTACTG
*
1840535 TTAACATTTAAAAATATAATACTATAATATATTAATATAA
1 TTAACATTTAAAAATAGAATACTATAATATATTAATATAA
1840575 TTAACATTTAAAAATAGAATACTATAATATATTAATA
1 TTAACATTTAAAAATAGAATACTATAATATATTAATA
1840612 ATTAATTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (40 bp):
TTAACATTTAAAAATAGAATACTATAATATATTAATATAA
Found at i:1857589 original size:111 final size:110
Alignment explanation
Indices: 1857462--1857670 Score: 339
Period size: 111 Copynumber: 1.9 Consensus size: 110
1857452 GTCAAAGGTT
* *
1857462 AAGCAAAGTATTAATTATGGATTGATCAAGCAT-TTTGGATTAATCTCAACCACACTTCTTAATT
1 AAGCAAAGTATTAATTATCGATTGATCAAGCATATAT-GATTAATCTCAACCACACTTCTTAATT
* **
1857526 AATTAGCTCTTTAATATCTTAAAGACATCTTCTTTTCATTATTGCTG
65 AATTAACTCTTTAATATCACAAAGACATC-TCTTTTCATTATTGCTG
1857573 AAGCAAAGTATTAATTATCGATTGATCAAGCATATATGATTAATCTCAACCACACTTCTTAATTA
1 AAGCAAAGTATTAATTATCGATTGATCAAGCATATATGATTAATCTCAACCACACTTCTTAATTA
*
1857638 ATTAACTCTTTTATATCACAAAGACATCTCTTT
66 ATTAACTCTTTAATATCACAAAGACATCTCTTT
1857671 CTTTCCATTA
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
110 5 0.05
111 84 0.92
112 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (110 bp):
AAGCAAAGTATTAATTATCGATTGATCAAGCATATATGATTAATCTCAACCACACTTCTTAATTA
ATTAACTCTTTAATATCACAAAGACATCTCTTTTCATTATTGCTG
Found at i:1859875 original size:21 final size:21
Alignment explanation
Indices: 1859850--1859901 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1859840 TGAAATATGG
* *
1859850 ATTTTATTTTTTTAATAAATA
1 ATTTTATTTGTTTAACAAATA
* *
1859871 ATTTTAGTTGTTTACCAAATA
1 ATTTTATTTGTTTAACAAATA
1859892 ATTTTTATTT
1 A-TTTTATTT
1859902 AAAAAATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (21 bp):
ATTTTATTTGTTTAACAAATA
Found at i:1868034 original size:312 final size:312
Alignment explanation
Indices: 1867469--1868094 Score: 1162
Period size: 312 Copynumber: 2.0 Consensus size: 312
1867459 ATTTTCTCTC
1867469 CATTCCCCCAATTTGTAAATATTCTTGTGATTGCTGGTTACCATTGCCACTTCAGCTTTTTCCTA
1 CATTCCCCCAATTTGTAAATATTCTTGTGATTGCTGGTTACCATTGCCACTTCAGCTTTTTCCTA
*
1867534 TCAATGACCAAGATTAGAGTCACAATATCTAACAGCAATATAGGAGTCACACACCTAATGTTTCG
66 TCAATGACCAAGATTAGAGTCACAATATCTAACAGCAATATAGGAGTCACACACCTAATGTTCCG
* * *
1867599 CACGCTATAATCATCACCCTCTAATTGATCTCTAAAGGTATGTGCTGCCCAACTAAATATCGAAA
131 CACACTATAATCATCACCCTCTAATTGATCTCTAAAGGTATGCGCTGCCAAACTAAATATCGAAA
1867664 CTTTGCACCCGCACACAAGGACCGTCCCCAAAGACAAAACTGCCGTGAAGCATGAGAGAGACAAA
196 CTTTGCACCCGCACACAAGGACCGTCCCCAAAGACAAAACTGCCGTGAAGCATGAGAGAGACAAA
*
1867729 ACAATTAAGGAATGCTCCAGGAGCAAAATGGGCAGTAACACTTCTATTATTT
261 ACAATTAAGGAATGCTCCAGGAGCAAAATGGACAGTAACACTTCTATTATTT
**
1867781 CATTCCCCCAATTTGTAAATATTCTTGTGATTGCTGGTTACCATTGCCGTTTCAGCTTTTTCCTA
1 CATTCCCCCAATTTGTAAATATTCTTGTGATTGCTGGTTACCATTGCCACTTCAGCTTTTTCCTA
*
1867846 TCAATGACCAAGATTAGAGTCACAATATCTAACAGCAATATAGGAGTCACGCACCTAATGTTCCG
66 TCAATGACCAAGATTAGAGTCACAATATCTAACAGCAATATAGGAGTCACACACCTAATGTTCCG
1867911 CACACTATAATCATCACCCTCTAATTGATCTCTAAAGGTATGCGCTGCCAAACTAAATATCGAAA
131 CACACTATAATCATCACCCTCTAATTGATCTCTAAAGGTATGCGCTGCCAAACTAAATATCGAAA
*
1867976 CTTTGCACCCGCATACAAGGACCGTCCCCAAAGACAAAACTGCCGTGAAGCATGAGAGAGACAAA
196 CTTTGCACCCGCACACAAGGACCGTCCCCAAAGACAAAACTGCCGTGAAGCATGAGAGAGACAAA
*
1868041 ACAATTAAGGAATGCTCCAGGAGCAAGATGGACAGTAACACTTCTATTATTT
261 ACAATTAAGGAATGCTCCAGGAGCAAAATGGACAGTAACACTTCTATTATTT
1868093 CA
1 CA
1868095 ACGTTAAGAA
Statistics
Matches: 304, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
312 304 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (312 bp):
CATTCCCCCAATTTGTAAATATTCTTGTGATTGCTGGTTACCATTGCCACTTCAGCTTTTTCCTA
TCAATGACCAAGATTAGAGTCACAATATCTAACAGCAATATAGGAGTCACACACCTAATGTTCCG
CACACTATAATCATCACCCTCTAATTGATCTCTAAAGGTATGCGCTGCCAAACTAAATATCGAAA
CTTTGCACCCGCACACAAGGACCGTCCCCAAAGACAAAACTGCCGTGAAGCATGAGAGAGACAAA
ACAATTAAGGAATGCTCCAGGAGCAAAATGGACAGTAACACTTCTATTATTT
Found at i:1882596 original size:29 final size:30
Alignment explanation
Indices: 1882564--1882623 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1882554 ATTCAATTGA
*
1882564 TTAATAAAATT-ATTTTTAAAATATAATAT
1 TTAATAAAATTAAATTTTAAAATATAATAT
* * *
1882593 TTAATAAATTTAAATTTTAAATTTTAATAT
1 TTAATAAAATTAAATTTTAAAATATAATAT
1882623 T
1 T
1882624 ACAAATTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTAATAAAATTAAATTTTAAAATATAATAT
Found at i:1886964 original size:2 final size:2
Alignment explanation
Indices: 1886957--1886988 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1886947 TGCATGGCAT
*
1886957 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1886989 TCTAGAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1887442 original size:2 final size:2
Alignment explanation
Indices: 1887435--1887459 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1887425 GGACAGCGCT
1887435 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 T
1887460 GTTTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1888376 original size:12 final size:12
Alignment explanation
Indices: 1888359--1888383 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1888349 TTTTCAATTT
1888359 AAAAAAAAAAGA
1 AAAAAAAAAAGA
1888371 AAAAAAAAAAGA
1 AAAAAAAAAAGA
1888383 A
1 A
1888384 GACGTTGAGT
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:1894847 original size:19 final size:19
Alignment explanation
Indices: 1894803--1894847 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1894793 AGCCTGAATA
*
1894803 CGAAAAACCACATCTCCAC
1 CGAAAACCCACATCTCCAC
1894822 CGAAAACCCACATCTCCAC
1 CGAAAACCCACATCTCCAC
1894841 CGAAAAC
1 CGAAAAC
1894848 GGTCACGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.42, C:0.42, G:0.07, T:0.09
Consensus pattern (19 bp):
CGAAAACCCACATCTCCAC
Found at i:1902040 original size:16 final size:16
Alignment explanation
Indices: 1902021--1902051 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1902011 AATTAATTTT
*
1902021 AAATTAAGTTTTTATA
1 AAATTAAATTTTTATA
1902037 AAATTAAATTTTTAT
1 AAATTAAATTTTTAT
1902052 GATTTTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
AAATTAAATTTTTATA
Found at i:1904576 original size:20 final size:19
Alignment explanation
Indices: 1904529--1904573 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1904519 TCGAACTAAG
* * *
1904529 TTATATATATTTTTAATTT
1 TTATAAATATTTTAAAATT
1904548 TTATAAATATTTTAAAATT
1 TTATAAATATTTTAAAATT
1904567 TTATAAA
1 TTATAAA
1904574 ATAAAAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATAAATATTTTAAAATT
Found at i:1915776 original size:15 final size:14
Alignment explanation
Indices: 1915756--1915787 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1915746 CTAATTTTAA
1915756 AATATAAATAATTAT
1 AATATAAATAA-TAT
1915771 AATATAAATAATAT
1 AATATAAATAATAT
1915785 AAT
1 AAT
1915788 TTTAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATAAATAATAT
Found at i:1926058 original size:33 final size:32
Alignment explanation
Indices: 1925996--1926064 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 32
1925986 CGATATAAAA
*
1925996 ATATAAAATATAATTTTTTATTTTATTAAATTT
1 ATATAAAATATAATTTATTATTTTATTAAA-TT
*
1926029 ATATATAATAATAA-TTATTATTATT-TTAAATT
1 ATATAAAAT-ATAATTTATTATT-TTATTAAATT
1926061 ATAT
1 ATAT
1926065 TATATTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 6 0.19
33 20 0.62
34 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
ATATAAAATATAATTTATTATTTTATTAAATT
Found at i:1926060 original size:16 final size:15
Alignment explanation
Indices: 1926041--1926092 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
1926031 ATATAATAAT
1926041 AATTATTATTATTTTA
1 AATTA-TATTATTTTA
1926057 AATTATATTATATTTA
1 AATTATATTAT-TTTA
*
1926073 TATTATA-T-TTTTA
1 AATTATATTATTTTA
1926086 AATTATA
1 AATTATA
1926093 CTTTTATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 10 0.30
14 1 0.03
15 7 0.21
16 15 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTATATTATTTTA
Found at i:1928218 original size:12 final size:13
Alignment explanation
Indices: 1928189--1928216 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1928179 AATCAAAATA
1928189 AAATTTTTATTAT
1 AAATTTTTATTAT
1928202 AAATTTTTATTAT
1 AAATTTTTATTAT
1928215 AA
1 AA
1928217 TTACAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AAATTTTTATTAT
Found at i:1929594 original size:21 final size:21
Alignment explanation
Indices: 1929560--1929599 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1929550 TGAAACTCAA
*
1929560 AAAATTTATAAATTTTATTTT
1 AAAATTTATAAATTATATTTT
* *
1929581 AAAATTTGTTAATTATATT
1 AAAATTTATAAATTATATT
1929600 ATTTTATTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
AAAATTTATAAATTATATTTT
Found at i:1929669 original size:14 final size:16
Alignment explanation
Indices: 1929645--1929676 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1929635 TTGATCAACA
1929645 AATTATTGAGAC-AAT
1 AATTATTGAGACGAAT
1929660 AATT-TTGAGACGAAT
1 AATTATTGAGACGAAT
1929675 AA
1 AA
1929677 AGTATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (16 bp):
AATTATTGAGACGAAT
Found at i:1937554 original size:14 final size:14
Alignment explanation
Indices: 1937535--1937586 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1937525 AATATTTTTC
1937535 AATAAATTATTTAT
1 AATAAATTATTTAT
*
1937549 AATAAATATATTTTT
1 AATAAAT-TATTTAT
* *
1937564 GAATAATTTAATTAT
1 -AATAAATTATTTAT
1937579 AATAAATT
1 AATAAATT
1937587 TTACTTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 14 0.45
15 11 0.35
16 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
AATAAATTATTTAT
Found at i:1937560 original size:30 final size:30
Alignment explanation
Indices: 1937526--1937585 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1937516 GTATTTTGCA
*
1937526 ATATTTTTCAATAAATTATTTATAATAAAT
1 ATATTTTTCAATAAATTAATTATAATAAAT
* *
1937556 ATATTTTTGAATAATTTAATTATAATAAAT
1 ATATTTTTCAATAAATTAATTATAATAAAT
1937586 TTTACTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
ATATTTTTCAATAAATTAATTATAATAAAT
Found at i:1939606 original size:24 final size:24
Alignment explanation
Indices: 1939579--1939625 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1939569 ACTCTACACT
*
1939579 AATATATCTGTTTCTCTTTCTATG
1 AATATATCTGTTACTCTTTCTATG
1939603 AATATATCTGTTACTCTTTCTAT
1 AATATATCTGTTACTCTTTCTAT
1939626 TAGGAACTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.53
Consensus pattern (24 bp):
AATATATCTGTTACTCTTTCTATG
Found at i:1951873 original size:21 final size:22
Alignment explanation
Indices: 1951835--1951886 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
1951825 ACCGAAATTA
1951835 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
1951857 ATAAAATATTA-TTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
1951878 AT-AAATATT
1 ATAAAATATT
1951887 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 12 0.40
22 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:1951928 original size:12 final size:14
Alignment explanation
Indices: 1951874--1951932 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
1951864 ATTATTTTTA
* *
1951874 AAATATAAATATTT
1 AAATATATATAATT
* *
1951888 AAAAATATCATTATAT
1 AAATATAT-ATAAT-T
1951904 AAATATATATAATT
1 AAATATATATAATT
1951918 AAATA-AT-TAATT
1 AAATATATATAATT
1951930 AAA
1 AAA
1951933 AAATAATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 8 0.22
13 2 0.05
14 12 0.32
15 7 0.19
16 8 0.22
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATATATAATT
Found at i:1952037 original size:16 final size:16
Alignment explanation
Indices: 1952016--1952067 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1952006 TATTATTTTT
*
1952016 AAAATATAAATATTTA
1 AAAATATAAATATATA
* *
1952032 AAAATATCATTATATA
1 AAAATATAAATATATA
* *
1952048 AAAATATATATAAATA
1 AAAATATAAATATATA
1952064 AAAA
1 AAAA
1952068 ATTAAATAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATATAAATATATA
Found at i:1954016 original size:18 final size:19
Alignment explanation
Indices: 1953995--1954045 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
1953985 ATATACTTTT
1953995 TAAAATATATTTAAAAAA-
1 TAAAATATATTTAAAAAAG
*
1954013 TAAAA-ATAATTAAAAAAG
1 TAAAATATATTTAAAAAAG
1954031 TAAAACATATATTTA
1 T-AAA-ATATATTTA
1954046 TCTTGTAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 11 0.41
18 6 0.22
19 3 0.11
20 1 0.04
21 6 0.22
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
TAAAATATATTTAAAAAAG
Found at i:1958118 original size:21 final size:21
Alignment explanation
Indices: 1958061--1958118 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 21
1958051 TTGTAATCAT
*
1958061 TTTTAATATAATTTTAATAAC
1 TTTTAATATAATTTTGATAAC
*
1958082 TTTTGTAATA-CA-TTTGATGAA-
1 -TTT-TAATATAATTTTGAT-AAC
1958103 TTTTAATATAATTTTG
1 TTTTAATATAATTTTG
1958119 GTAATCTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
19 5 0.17
20 4 0.14
21 9 0.31
22 6 0.21
23 5 0.17
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTTAATATAATTTTGATAAC
Found at i:1967234 original size:28 final size:28
Alignment explanation
Indices: 1967200--1967257 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1967190 TTAGTATTAT
* * * *
1967200 TATAAAAAATAT-TATGAGTAAATGAAA
1 TATAAAAAACATATATAAGAAAATCAAA
1967227 TATAAAAAACATATATAAGAAAATCAAA
1 TATAAAAAACATATATAAGAAAATCAAA
1967255 TAT
1 TAT
1967258 TGAAAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (28 bp):
TATAAAAAACATATATAAGAAAATCAAA
Found at i:1967998 original size:22 final size:21
Alignment explanation
Indices: 1967973--1968083 Score: 77
Period size: 22 Copynumber: 5.2 Consensus size: 21
1967963 TATTATATCC
1967973 TAATGAAATTATAATTATTAAA
1 TAAT-AAATTATAATTATTAAA
* * *
1967995 TAATCAATTGT-A--ACTAAA
1 TAATAAATTATAATTATTAAA
* *
1968013 TAATCAAATTCATATATAATGAAA
1 TAAT-AAATT-ATA-ATTATTAAA
1968037 -AATAAAATTATAATTATTAAA
1 TAAT-AAATTATAATTATTAAA
* *
1968058 TAATTAACTTATAATTACTAAA
1 TAA-TAAATTATAATTATTAAA
1968080 TAAT
1 TAAT
1968084 CGATTAAGAT
Statistics
Matches: 69, Mismatches: 12, Indels: 17
0.70 0.12 0.17
Matches are distributed among these distances:
18 9 0.13
19 4 0.06
20 2 0.03
21 13 0.19
22 28 0.41
23 9 0.13
24 4 0.06
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (21 bp):
TAATAAATTATAATTATTAAA
Found at i:1986843 original size:16 final size:16
Alignment explanation
Indices: 1986822--1986862 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1986812 AATTAACAAT
1986822 ATATATATACACACAC
1 ATATATATACACACAC
* *
1986838 ATATATATACACAGAT
1 ATATATATACACACAC
1986854 ATATATATA
1 ATATATATA
1986863 TATATATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (16 bp):
ATATATATACACACAC
Found at i:1986871 original size:14 final size:14
Alignment explanation
Indices: 1986824--1986860 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1986814 TTAACAATAT
* *
1986824 ATATATACACACAC
1 ATATATATACACAG
1986838 ATATATATACACAG
1 ATATATATACACAG
1986852 ATATATATA
1 ATATATATA
1986861 TATATATATA
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:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (14 bp):
ATATATATACACAG
Found at i:1997449 original size:161 final size:161
Alignment explanation
Indices: 1997168--1998032 Score: 879
Period size: 161 Copynumber: 5.4 Consensus size: 161
1997158 CTAATCACCC
* * * * * * *
1997168 TTAACAGTTTTGATAGTTTCAATATATAATATTAAACTTGTTCGAATAATTAAACTT-GATTTTC
1 TTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAATAATTGAACTTAG-TTTTC
* * ** * *
1997232 ACAGTTGATATGTATGAAAAAGCTAACATTTACG-CATGTTTA-AGACTTTCTATGCCGTTAAAA
65 ACAGTTGATATGTGTGAAAAAGTTAATGTTTACGTC-TGTTTAGA-ACTTTTTATGTCGTTAAAA
* * **
1997295 GGTAAAATTATAATTTTGCTATTATTATTTTATT
128 GGTAAAAATACAAAATTGCTATTATTATTTTATT
1997329 TTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAATAATTGAACTTAGTTTTCA
1 TTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAATAATTGAACTTAGTTTTCA
* * *
1997394 CAGTTGATATGTGTAAAAAAGTTAATGTTTATGTCTGTTTAGAACTTTTTATGCCGTTAAAAGGT
66 CAGTTGATATGTGTGAAAAAGTTAATGTTTACGTCTGTTTAGAACTTTTTATGTCGTTAAAAGGT
* * * *
1997459 AAAAATATAAAATTACTATTATTGTTCTATT
131 AAAAATACAAAATTGCTATTATTATTTTATT
* * * * * * * *
1997490 TTAACAGTTTTGATAGCTTCGATATATGATAATAAATTTGTCCAGATGATTGAACTTAGTTTTTA
1 TTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAATAATTGAACTTAGTTTTCA
** * ** * * * * * *
1997555 TGGTTAATATGTGTGAAAAA-TTTGTCGTTTACATATATTTAAAACTTTTTTTGTCGTTAAAAGA
66 CAGTTGATATGTGTGAAAAAGTTAAT-GTTTACGTCTGTTTAGAACTTTTTATGTCGTTAAAAGG
1997619 TAAAAATACAAAATTGCTATTATTATTTTATT
130 TAAAAATACAAAATTGCTATTATTATTTTATT
* * * * *
1997651 TTAACAGTTTAGATAGCTTCAATACATGATATTAAACTTATCCGAATAATTAAACTTGGTTTTCA
1 TTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAATAATTGAACTTAGTTTTCA
* * * * * *
1997716 CAGTTGATAGGTGTGAAAAAATTAATGTTTA-GTTTGTTTAGGACTTTTTACGTTGTTAAAAAGG
66 CAGTTGATATGTGTGAAAAAGTTAATGTTTACGTCTGTTTAGAACTTTTTATGTCGTT-AAAAGG
* * *
1997780 TAAAAATGC-AAATTGCTATTATTGTTATATT
130 TAAAAATACAAAATTGCTATTATTATTTTATT
* * * * * *
1997811 TTAACAGTTTGGATAGCTTCAATATATGATAATAAATTTATCCAAATTATTGAACTT-GGTTTCT
1 TTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAATAATTGAACTTAGTTTTC-
* * * * * * *
1997875 ATAGTTAATAAGTATGAAAAAG-T--TGTTTACGTCTATTTAGGACTTTTT-TGTCGTTAAAAGA
65 ACAGTTGATATGTGTGAAAAAGTTAATGTTTACGTCTGTTTAGAACTTTTTATGTCGTTAAAAGG
* * * * *
1997936 CAAAAATGCAAATTTGCTGTTATTATTTTGTT
130 TAAAAATACAAAATTGCTATTATTATTTTATT
* * * * *
1997968 TTAACAGTTTGAATAGTTTCAATACATGATATTAAACTTGTCCAAATGATTGAAATTAATTTTCA
1 TTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAATAATTGAACTTAGTTTTCA
1998033 TGATTAATAT
Statistics
Matches: 584, Mismatches: 110, Indels: 24
0.81 0.15 0.03
Matches are distributed among these distances:
156 13 0.02
157 78 0.13
158 20 0.03
159 6 0.01
160 108 0.18
161 353 0.60
162 6 0.01
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (161 bp):
TTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTGTCCAAATAATTGAACTTAGTTTTCA
CAGTTGATATGTGTGAAAAAGTTAATGTTTACGTCTGTTTAGAACTTTTTATGTCGTTAAAAGGT
AAAAATACAAAATTGCTATTATTATTTTATT
Found at i:1997780 original size:322 final size:316
Alignment explanation
Indices: 1997287--1998032 Score: 994
Period size: 322 Copynumber: 2.3 Consensus size: 316
1997277 CTTTCTATGC
* * * *
1997287 CGTTAAAAGGTAAAATTATAATTTTGCTATTATTATTTTATTTTAACAGTTTGGATAGCTTCAAT
1 CGTTAAAAGATAAAAATACAAATTTGCTATTATTATTTTATTTTAACAGTTT-GATAGCTTCAAT
* * *
1997352 ACATGATATTAAACTTGTCCAAATAATTGAACTTAGTTTTCACAGTTGATATGTGTAAAAAAGTT
65 ACATGATATTAAACTTATCCAAATAATTAAACTTAGTTTTCACAGTTGATAGGTGTAAAAAAGTT
* *
1997417 AATGTTTATGTCTGTTTAGAACTTTTTATGCCGTTAAAAGGTAAAAATATAAAATTACTATTATT
130 AATGTTTATGTCTGTTTAGAACTTTTTACGCCGTTAAAAGGTAAAAAT-GAAAATTACTATTATT
* * * * *
1997482 GTTCTATTTTAACAGTTTTGATAGCTTCGATATATGATAATAAATTTGTCCAGATGATTGAACTT
194 GTTATATTTTAACAGTTTGGATAGCTTCAATATATGATAATAAATTTATCCAAATGATTGAACTT
* * * *
1997547 AGTTTTTATGGTTAATATGTGTGAAAAATTTGTCGTTTACATATATTTAAAACTTTTTTTGT
259 AGTTTCTATAGTTAATAAGTATGAAAAA---GTCGTTTACATATATTTAAAAC-TTTTTTGT
*
1997609 CGTTAAAAGATAAAAATACAAAATTGCTATTATTATTTTATTTTAACAGTTTAGATAGCTTCAAT
1 CGTTAAAAGATAAAAATACAAATTTGCTATTATTATTTTATTTTAACAGTTT-GATAGCTTCAAT
* *
1997674 ACATGATATTAAACTTATCCGAATAATTAAACTTGGTTTTCACAGTTGATAGGTGTGAAAAAA-T
65 ACATGATATTAAACTTATCCAAATAATTAAACTTAGTTTTCACAGTTGATAGGTGT-AAAAAAGT
* * ** * *
1997738 TAATGTTTA-GTTTGTTTAGGACTTTTTACGTTGTTAAAAAGGTAAAAATGCAAATTGCTATTAT
129 TAATGTTTATGTCTGTTTAGAACTTTTTACGCCGTT-AAAAGGTAAAAATGAAAATTACTATTAT
*
1997802 TGTTATATTTTAACAGTTTGGATAGCTTCAATATATGATAATAAATTTATCCAAATTATTGAACT
193 TGTTATATTTTAACAGTTTGGATAGCTTCAATATATGATAATAAATTTATCCAAATGATTGAACT
* * * * **
1997867 TGGTTTCTATAGTTAATAAGTATGAAAAAGTTGTTTACGTCTATTTAGGACTTTTTTGT
258 TAGTTTCTATAGTTAATAAGTATGAAAAAGTCGTTTACATATATTTAAAACTTTTTTGT
* * * * *
1997926 CGTTAAAAGACAAAAATGCAAATTTGCTGTTATTATTTTGTTTTAACAGTTTGAATAGTTTCAAT
1 CGTTAAAAGATAAAAATACAAATTTGCTATTATTATTTTATTTTAACAGTTTG-ATAGCTTCAAT
* * *
1997991 ACATGATATTAAACTTGTCCAAATGATTGAAA-TTAATTTTCA
65 ACATGATATTAAACTTATCCAAATAATT-AAACTTAGTTTTCA
1998033 TGATTAATAT
Statistics
Matches: 374, Mismatches: 46, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
316 1 0.00
317 98 0.26
318 20 0.05
321 116 0.31
322 133 0.36
323 6 0.02
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (316 bp):
CGTTAAAAGATAAAAATACAAATTTGCTATTATTATTTTATTTTAACAGTTTGATAGCTTCAATA
CATGATATTAAACTTATCCAAATAATTAAACTTAGTTTTCACAGTTGATAGGTGTAAAAAAGTTA
ATGTTTATGTCTGTTTAGAACTTTTTACGCCGTTAAAAGGTAAAAATGAAAATTACTATTATTGT
TATATTTTAACAGTTTGGATAGCTTCAATATATGATAATAAATTTATCCAAATGATTGAACTTAG
TTTCTATAGTTAATAAGTATGAAAAAGTCGTTTACATATATTTAAAACTTTTTTGT
Found at i:1998133 original size:321 final size:321
Alignment explanation
Indices: 1997309--1998118 Score: 904
Period size: 322 Copynumber: 2.5 Consensus size: 321
1997299 AAATTATAAT
*
1997309 TTTGCTATTATTATTTTATTTTAACAGTTTGGATAGCTTCAATACATGATATTAAACTTGTCCAA
1 TTTGCTATTATTATTTTATTTTAACAGTTTGAATAGCTTCAATACATGATATTAAACTTGTCCAA
* *
1997374 ATAATTGAACTTAGTTTTCACAGTTGATATGTGT--AA--AAAA-GTTAATGTTTA-TGTCTGTT
66 ATAATTGAAATTAGTTTTCACAGTTGATATGTGTGAAAGTAAAATGTTTATGTTTACT-T-TGTT
* * *
1997433 -TAGAACTTTTTATGCCGTTAAAAGGTAAAAATATAAAATTACTATTATTGTTCTATTTTAACAG
129 AAAG-ACTTTTTATGCTGTTAAAAGGTAAAAATAT--AATT-CTATTATTGTTATATTTTAACAG
* * * * * *
1997497 TTTTGATAGCTTCGATATATGATAATAAATTTGTCCAGATGATTGAACTTAGTTTTTATGGTTAA
190 TTTGGATAGCTTCAATATATGATAATAAATTTATCCAAATGATTGAACTTAGTTTCTATAGTTAA
* * *
1997562 TATGTGTGAAAAATTTGTCGTTTACATATATTTAAAACTTTTTTTGTCGTTAAAAGATAAAAATA
255 TAAGTATGAAAAA--TGTCGTTTACATATATTTAAAACTTTTTTTGTCGTTAAAAGACAAAAATA
1997627 CAAA
318 CAAA
* * *
1997631 ATTGCTATTATTATTTTATTTTAACAGTTT-AGATAGCTTCAATACATGATATTAAACTTATCCG
1 TTTGCTATTATTATTTTATTTTAACAGTTTGA-ATAGCTTCAATACATGATATTAAACTTGTCCA
* * * *
1997695 AATAATT-AAACTTGGTTTTCACAGTTGATAGGTGTG-AA--AAAA--TTAATGTTTAGTTTGTT
65 AATAATTGAAA-TTAGTTTTCACAGTTGATATGTGTGAAAGTAAAATGTTTATGTTTACTTTGTT
* * * *
1997754 TAGGACTTTTTACGTTGTTAAAAAGGTAAAAATGCA-AATTGCTATTATTGTTATATTTTAACAG
129 AAAGACTTTTTATGCTGTT-AAAAGGTAAAAAT--ATAATT-CTATTATTGTTATATTTTAACAG
* *
1997818 TTTGGATAGCTTCAATATATGATAATAAATTTATCCAAATTATTGAACTTGGTTTCTATAGTTAA
190 TTTGGATAGCTTCAATATATGATAATAAATTTATCCAAATGATTGAACTTAGTTTCTATAGTTAA
* * * ** *
1997883 TAAGTATGAAAAA-GTTGTTTACGTCTATTTAGGAC-TTTTTTGTCGTTAAAAGACAAAAATGCA
255 TAAGTATGAAAAATGTCGTTTACATATATTTAAAACTTTTTTTGTCGTTAAAAGACAAAAATACA
1997946 AA
320 AA
* * *
1997948 TTTGCTGTTATTATTTTGTTTTAACAGTTTGAATAGTTTCAATACATGATATTAAACTTGTCCAA
1 TTTGCTATTATTATTTTATTTTAACAGTTTGAATAGCTTCAATACATGATATTAAACTTGTCCAA
* * * * *
1998013 ATGATTGAAATTAATTTTCA-TGATTAATATGTATGAAAGGGTAAAATGCTGTTATTGTTTACAT
66 ATAATTGAAATTAGTTTTCACAG-TTGATATGTGTGAAA--GTAAAATG-T-TTA-TGTTTAC-T
1998077 TTGTTAAAGAC-TTTTATGCTGTT-AAAGGATAAAAATATAATT
124 TTGTTAAAGACTTTTTATGCTGTTAAAAGG-TAAAAATATAATT
1998119 TTACAGTTAT
Statistics
Matches: 414, Mismatches: 50, Indels: 45
0.81 0.10 0.09
Matches are distributed among these distances:
316 1 0.00
317 107 0.26
318 23 0.06
321 112 0.27
322 117 0.28
323 7 0.02
324 2 0.00
325 10 0.02
326 9 0.02
327 16 0.04
328 10 0.02
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (321 bp):
TTTGCTATTATTATTTTATTTTAACAGTTTGAATAGCTTCAATACATGATATTAAACTTGTCCAA
ATAATTGAAATTAGTTTTCACAGTTGATATGTGTGAAAGTAAAATGTTTATGTTTACTTTGTTAA
AGACTTTTTATGCTGTTAAAAGGTAAAAATATAATTCTATTATTGTTATATTTTAACAGTTTGGA
TAGCTTCAATATATGATAATAAATTTATCCAAATGATTGAACTTAGTTTCTATAGTTAATAAGTA
TGAAAAATGTCGTTTACATATATTTAAAACTTTTTTTGTCGTTAAAAGACAAAAATACAAA
Found at i:2010341 original size:2 final size:2
Alignment explanation
Indices: 2010334--2010365 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2010324 TTTCTGGGCC
2010334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2010366 TCTTTTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2010880 original size:30 final size:32
Alignment explanation
Indices: 2010822--2010882 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
2010812 TTATATAAAA
* *
2010822 ATATAAAATATATTTTTTAATTTATTAAATTT
1 ATATAAAATATATTTTTAAAATTATTAAATTT
2010854 ATATAAAAT-TATTTTTAAAATT-TTAAATT
1 ATATAAAATATATTTTTAAAATTATTAAATT
2010883 ACATTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 7 0.26
31 11 0.41
32 9 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
ATATAAAATATATTTTTAAAATTATTAAATTT
Found at i:2019843 original size:14 final size:14
Alignment explanation
Indices: 2019826--2019868 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
2019816 ATATTTATAA
*
2019826 ATATATAAAAATTT
1 ATATATAACAATTT
*
2019840 ATATATAACAATAT
1 ATATATAACAATTT
2019854 -TAT-TAACAATTT
1 ATATATAACAATTT
2019866 ATA
1 ATA
2019869 AAATAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 8 0.32
13 5 0.20
14 12 0.48
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATATAACAATTT
Found at i:2019846 original size:22 final size:22
Alignment explanation
Indices: 2019812--2019882 Score: 61
Period size: 26 Copynumber: 3.0 Consensus size: 22
2019802 GTCTTATTAT
* *
2019812 AAATATATTTATAAATATATAA
1 AAATTTATATATAAATATATAA
2019834 AAATTTATATATAACAATATTATTAA
1 AAATTTATATAT-A-AATA-TA-TAA
* *
2019860 CAATTTATAAAATAAATATATAA
1 AAATTTAT-ATATAAATATATAA
2019883 TATATTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 10 0.25
23 4 0.10
24 6 0.15
25 6 0.15
26 11 0.28
27 3 0.08
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATTTATATATAAATATATAA
Found at i:2019889 original size:24 final size:23
Alignment explanation
Indices: 2019809--2019917 Score: 77
Period size: 22 Copynumber: 4.9 Consensus size: 23
2019799 GCAGTCTTAT
*
2019809 TATAAATATATTTAT-AAATATA
1 TATAAATATATTTATAAAATAAA
* * * *
2019831 TAAAAATTTATATATAACAAT-AT
1 TATAAATATATTTATAA-AATAAA
* *
2019854 TATTAACA-ATTTATAAAATAAA
1 TATAAATATATTTATAAAATAAA
*
2019876 TATATAATATATTTA-AAAATTAA
1 TATA-AATATATTTATAAAATAAA
*
2019899 -ATAAATAAATTTA-AAAATA
1 TATAAATATATTTATAAAATA
2019918 TAAAAATAAT
Statistics
Matches: 66, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
21 17 0.26
22 26 0.39
23 15 0.23
24 8 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TATAAATATATTTATAAAATAAA
Found at i:2019910 original size:21 final size:22
Alignment explanation
Indices: 2019861--2019928 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 22
2019851 TATTATTAAC
*
2019861 AATTTATAAAATAAATATATAATA
1 AATTTA-AAAATTAA-ATATAATA
*
2019885 TATTTAAAAATTAAATA-AATA
1 AATTTAAAAATTAAATATAATA
*
2019906 AATTTAAAAATATAAAAATAATA
1 AATTTAAAAAT-TAAATATAATA
2019929 TTATCAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 14 0.37
22 8 0.21
23 11 0.29
24 5 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AATTTAAAAATTAAATATAATA
Found at i:2019924 original size:24 final size:24
Alignment explanation
Indices: 2019861--2019926 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
2019851 TATTATTAAC
* *
2019861 AATTTATAAA-ATAAATATATAATA
1 AATTTAAAAATATAAAAATA-AATA
*
2019885 TATTTAAAAAT-T--AAATAAATA
1 AATTTAAAAATATAAAAATAAATA
2019906 AATTTAAAAATATAAAAATAA
1 AATTTAAAAATATAAAAATAA
2019927 TATTATCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 14 0.41
22 5 0.15
24 15 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AATTTAAAAATATAAAAATAAATA
Found at i:2020050 original size:17 final size:17
Alignment explanation
Indices: 2020024--2020058 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2020014 GCTTTGATTT
2020024 AAAAAGTTAAAATATAA
1 AAAAAGTTAAAATATAA
* *
2020041 AAAAATTTAAAATTTAA
1 AAAAAGTTAAAATATAA
2020058 A
1 A
2020059 TATTATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAAAGTTAAAATATAA
Found at i:2020240 original size:20 final size:21
Alignment explanation
Indices: 2020217--2020255 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2020207 AATATTATCT
*
2020217 AATATCA-ATTTTAATATAAA
1 AATATCATATTTAAATATAAA
*
2020237 AATATTATATTTAAATATA
1 AATATCATATTTAAATATA
2020256 TTATTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATCATATTTAAATATAAA
Found at i:2020987 original size:18 final size:18
Alignment explanation
Indices: 2020960--2020994 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2020950 ATTTTTTAAT
*
2020960 AAAATGAATTACAAATAA
1 AAAATAAATTACAAATAA
2020978 AAAATAAATTACAAATA
1 AAAATAAATTACAAATA
2020995 CTTTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAATAAATTACAAATAA
Found at i:2021763 original size:9 final size:10
Alignment explanation
Indices: 2021737--2021761 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2021727 TTATTTTTTT
2021737 ATTTTTATAA
1 ATTTTTATAA
2021747 ATTTTTATAA
1 ATTTTTATAA
2021757 ATTTT
1 ATTTT
2021762 ATTATTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:2021770 original size:9 final size:9
Alignment explanation
Indices: 2021727--2021777 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
2021717 TGCACACATT
2021727 TTATTTTT-
1 TTATTTTTA
2021735 TTATTTTTA
1 TTATTTTTA
*
2021744 TAAATTTTTA
1 T-TATTTTTA
* *
2021754 TAAATTTTA
1 TTATTTTTA
*
2021763 TTATTTTTC
1 TTATTTTTA
2021772 TTATTT
1 TTATTT
2021778 AAAATAAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
8 8 0.22
9 20 0.56
10 8 0.22
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (9 bp):
TTATTTTTA
Found at i:2023314 original size:19 final size:19
Alignment explanation
Indices: 2023290--2023337 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
2023280 CCATTCCCCC
* *
2023290 TTTTTTTATTTTTTTATGT
1 TTTTTTTATTATTTTATAT
2023309 TTTTTTTGA-TATTTTATAT
1 TTTTTTT-ATTATTTTATAT
*
2023328 TTTTTGTATT
1 TTTTTTTATT
2023338 CTGTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 22 0.92
20 1 0.04
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (19 bp):
TTTTTTTATTATTTTATAT
Found at i:2023337 original size:16 final size:17
Alignment explanation
Indices: 2023310--2023347 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2023300 TTTTTATGTT
*
2023310 TTTTTTGATATTTTATA
1 TTTTTTGATATTCTATA
*
2023327 TTTTTTG-TATTCTGTA
1 TTTTTTGATATTCTATA
2023343 TTTTT
1 TTTTT
2023348 ATTTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTTTGATATTCTATA
Found at i:2034699 original size:22 final size:23
Alignment explanation
Indices: 2034665--2034716 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
2034655 TATGTCTTAT
2034665 TTATTTTAGATA-TATAAAATTC
1 TTATTTTAGATATTATAAAATTC
** *
2034687 TTATTTTTTATATTTTAAAATT-
1 TTATTTTAGATATTATAAAATTC
*
2034709 ATATTTTA
1 TTATTTTA
2034717 TGATTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTATTTTAGATATTATAAAATTC
Found at i:2043617 original size:2 final size:2
Alignment explanation
Indices: 2043610--2043640 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2043600 CATATCTATC
*
2043610 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2043641 GGGATGACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.