Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 37
Found at i:1608085 original size:25 final size:23
Alignment explanation
Indices: 1608035--1608096 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
1608025 ATATACATAC
1608035 ATTT-TTATTTTTATATATATTT
1 ATTTATTATTTTTATATATATTT
*
1608057 -TTTATTATTTTATTTATACTATTT
1 ATTTATTATTTT-TATATA-TATTT
*
1608081 ATTTATT-TTATTATAT
1 ATTTATTATTTTTATAT
1608097 TTTTAATTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 3 0.09
22 7 0.21
23 9 0.27
24 8 0.24
25 6 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
ATTTATTATTTTTATATATATTT
Found at i:1608105 original size:21 final size:20
Alignment explanation
Indices: 1608035--1608101 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 20
1608025 ATATACATAC
*
1608035 ATTTTTATTT-TTATA-TAT
1 ATTTTTATTTATTTTATTAT
1608053 ATTTTT-TATTATTTTATTTAT
1 ATTTTTAT-TTATTTTA-TTAT
*
1608074 ACTATTTATTTATTTTATTAT
1 A-TTTTTATTTATTTTATTAT
1608095 ATTTTTA
1 ATTTTTA
1608102 ATTTCTTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.03
18 8 0.20
19 4 0.10
20 5 0.12
21 9 0.22
22 12 0.30
23 1 0.03
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTTATTTATTTTATTAT
Found at i:1608105 original size:25 final size:26
Alignment explanation
Indices: 1608040--1608126 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 26
1608030 CATACATTTT
* * *
1608040 TATTTTTATATATATTTTTTATTATTT
1 TATTTTTATATTTATTTATT-TTATTA
*
1608067 TATTTATACTATTTATTTATTTTATTA
1 TATTTTTA-TATTTATTTATTTTATTA
* *
1608094 TATTTTTA-ATTTCTTTGTTTTATTA
1 TATTTTTATATTTATTTATTTTATTA
1608119 TTATTTTT
1 -TATTTTT
1608127 CTTTTTTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
25 15 0.29
26 7 0.14
27 19 0.37
28 10 0.20
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.72
Consensus pattern (26 bp):
TATTTTTATATTTATTTATTTTATTA
Found at i:1608117 original size:20 final size:20
Alignment explanation
Indices: 1608076--1608135 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
1608066 TTATTTATAC
*
1608076 TATT-TATTTATTTTATTATAT
1 TATTATATTTCTTTT-TT-TAT
*
1608097 TTTTA-ATTTCTTTGTTTTAT
1 TATTATATTTCTTT-TTTTAT
*
1608117 TATTATTTTTCTTTTTTTA
1 TATTATATTTCTTTTTTTA
1608136 AAAAAACACT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 12 0.38
21 19 0.59
22 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (20 bp):
TATTATATTTCTTTTTTTAT
Found at i:1608202 original size:18 final size:18
Alignment explanation
Indices: 1608174--1608221 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1608164 TGTATATATA
*
1608174 TTTTATATTCATTT-ATT
1 TTTTTTATTCATTTCATT
1608191 TTATTTTATTCAATTTCATT
1 TT-TTTTATTC-ATTTCATT
1608211 TTTTTT-TTCAT
1 TTTTTTATTCAT
1608222 CCAATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 4 0.15
18 10 0.37
19 8 0.30
20 5 0.19
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTATTCATTTCATT
Found at i:1608226 original size:22 final size:24
Alignment explanation
Indices: 1608181--1608227 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
1608171 ATATTTTATA
* *
1608181 TTCATTTATTTTATTTTATTCAAT
1 TTCATTTATTTTATTTCATCCAAT
1608205 TTCATTT-TTTT-TTTCATCCAAT
1 TTCATTTATTTTATTTCATCCAAT
1608227 T
1 T
1608228 ATTTTATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 4 0.19
24 7 0.33
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (24 bp):
TTCATTTATTTTATTTCATCCAAT
Found at i:1609906 original size:17 final size:18
Alignment explanation
Indices: 1609864--1609909 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
1609854 TATTTGATTA
*
1609864 TTTATTTATTTTACTAAT
1 TTTATTTATTTTACAAAT
**
1609882 GATA-TTATTTTA-AAAT
1 TTTATTTATTTTACAAAT
1609898 TTTATTTATTTT
1 TTTATTTATTTT
1609910 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
16 5 0.23
17 15 0.68
18 2 0.09
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTATTTTACAAAT
Found at i:1609921 original size:22 final size:22
Alignment explanation
Indices: 1609889--1609930 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1609879 AATGATATTA
1609889 TTTTAAAATTTTAT-TTATTTT
1 TTTTAAAATTTTATGTTATTTT
1609910 TTTTAAAAATTTTATGTTATT
1 TTTT-AAAATTTTATGTTATT
1609931 AACGTGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTAAAATTTTATGTTATTTT
Found at i:1610662 original size:74 final size:75
Alignment explanation
Indices: 1610520--1610669 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 75
1610510 TTCACCCCTT
*
1610520 TGGTTTTTATTTCTATCTTTATTACATTTTTTTTTGCATAAAGTATACTGATTCGATGTTCTTTG
1 TGGTTTTTATTTCTATATTTATTACATTTTTTTTTGCATAAAGTATACTGATTCGATGTTCTTTG
1610585 TTTCCCTCGA
66 TTTCCCTCGA
*
1610595 TGGTTTTTATTTCTATATTTATTACATTTTTTTTTGCA-AAAGTATACTGATTCGATGTTGTTTG
1 TGGTTTTTATTTCTATATTTATTACATTTTTTTTTGCATAAAGTATACTGATTCGATGTTCTTTG
1610659 TTTCCCTCGA
66 TTTCCCTCGA
1610669 T
1 T
1610670 CCAGGTTCAT
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 36 0.49
75 37 0.51
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (75 bp):
TGGTTTTTATTTCTATATTTATTACATTTTTTTTTGCATAAAGTATACTGATTCGATGTTCTTTG
TTTCCCTCGA
Found at i:1616289 original size:31 final size:30
Alignment explanation
Indices: 1616214--1616296 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
1616204 AGAAACCCAC
* * *
1616214 CACAAC-AAACCAAAGAAAACAAAAGCCCT
1 CACAACAAAAACAAAGGAAACAAAAGCCAT
* * *
1616243 CACAGCAGAAGCAAAGGAAACAAAAGCTCAT
1 CACAACAAAAACAAAGGAAACAAAAGC-CAT
1616274 CACAACAAAAACAAA-GAAACAAA
1 CACAACAAAAACAAAGGAAACAAA
1616297 TATAGGGGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 5 0.11
30 25 0.57
31 14 0.32
ACGTcount: A:0.60, C:0.25, G:0.11, T:0.04
Consensus pattern (30 bp):
CACAACAAAAACAAAGGAAACAAAAGCCAT
Found at i:1626418 original size:22 final size:22
Alignment explanation
Indices: 1626370--1626419 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1626360 TTTCATAAAT
*
1626370 ATTATATTTTAATTAAATTACA
1 ATTATATTTTAACTAAATTACA
* * *
1626392 TTTATATTTTAACTAATTTATA
1 ATTATATTTTAACTAAATTACA
1626414 ATTATA
1 ATTATA
1626420 CCTGTAATAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTATATTTTAACTAAATTACA
Found at i:1630205 original size:28 final size:28
Alignment explanation
Indices: 1630165--1630220 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1630155 GTACAAAGAA
1630165 CGAATGAATTGAATCATTTGAATGCTTT
1 CGAATGAATTGAATCATTTGAATGCTTT
1630193 CGAATGAATTGAATCATTTGAATGCTTT
1 CGAATGAATTGAATCATTTGAATGCTTT
1630221 AAGATCATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (28 bp):
CGAATGAATTGAATCATTTGAATGCTTT
Found at i:1631878 original size:20 final size:19
Alignment explanation
Indices: 1631832--1631892 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
1631822 TTTAGTGTTT
1631832 AAATTTATTAA-TTTGAAA
1 AAATTTATTAATTTTGAAA
* *
1631850 AAATATATTCAATTTTGATA
1 AAATTTATT-AATTTTGAAA
* **
1631870 ATATTTATTAATTCAGAAA
1 AAATTTATTAATTTTGAAA
1631889 AAAT
1 AAAT
1631893 GTATAAAACT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
18 8 0.24
19 12 0.36
20 13 0.39
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (19 bp):
AAATTTATTAATTTTGAAA
Found at i:1632115 original size:38 final size:38
Alignment explanation
Indices: 1632063--1632148 Score: 129
Period size: 38 Copynumber: 2.3 Consensus size: 38
1632053 CCACGCAAAT
1632063 TTCGCAACTCTAATTACCGATATACATAAACACAACTA
1 TTCGCAACTCTAATTACCGATATACATAAACACAACTA
* **
1632101 TTCGCAACGT-TAATTATCGATATAGGTAAACACAACTA
1 TTCGCAAC-TCTAATTACCGATATACATAAACACAACTA
1632139 TTCGCAACTC
1 TTCGCAACTC
1632149 AGTTTTCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 1 0.02
38 41 0.95
39 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.28
Consensus pattern (38 bp):
TTCGCAACTCTAATTACCGATATACATAAACACAACTA
Found at i:1632175 original size:20 final size:20
Alignment explanation
Indices: 1632152--1632195 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1632142 GCAACTCAGT
1632152 TTTCAAATTAGCAACGCGAA
1 TTTCAAATTAGCAACGCGAA
** * *
1632172 TTTCATTTTCGCAACTCGAA
1 TTTCAAATTAGCAACGCGAA
1632192 TTTC
1 TTTC
1632196 GCAACCTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (20 bp):
TTTCAAATTAGCAACGCGAA
Found at i:1634355 original size:20 final size:20
Alignment explanation
Indices: 1634326--1634382 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
1634316 TTTTAAATTT
* *
1634326 TATGTGATAAAATTATAGTG
1 TATGTAATAAAATTATAATG
* *
1634346 TATGTTATAATAATAATAATG
1 TATGTAATAA-AATTATAATG
1634367 TAT-TAATAAAAATTAT
1 TATGTAAT-AAAATTAT
1634383 TAAAATTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TATGTAATAAAATTATAATG
Found at i:1647965 original size:33 final size:32
Alignment explanation
Indices: 1647927--1647999 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
1647917 TATGCTTCTC
1647927 TAATATAATATAATATTAT-TTTTTTAGTTAATA
1 TAATATAATATAATATTATGTTTTTTAGTT--TA
*
1647960 TAATAT--TATAATTTTATGTTTTTTAGTTTA
1 TAATATAATATAATATTATGTTTTTTAGTTTA
*
1647990 TTATATAATA
1 TAATATAATA
1648000 ACATTATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
30 7 0.20
31 10 0.29
32 12 0.34
33 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (32 bp):
TAATATAATATAATATTATGTTTTTTAGTTTA
Found at i:1647974 original size:23 final size:23
Alignment explanation
Indices: 1647932--1647975 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1647922 TTCTCTAATA
**
1647932 TAATATAATATTATTTTTTTAGT
1 TAATATAATATTATAATTTTAGT
1647955 TAATATAATATTATAATTTTA
1 TAATATAATATTATAATTTTA
1647976 TGTTTTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TAATATAATATTATAATTTTAGT
Found at i:1649006 original size:32 final size:32
Alignment explanation
Indices: 1648979--1649073 Score: 111
Period size: 35 Copynumber: 2.8 Consensus size: 32
1648969 CTTCGATATG
1648979 AATTAAATAAAAAATATATATTTTTCGAATCA
1 AATTAAATAAAAAATATATATTTTTCGAATCA
* *
1649011 AATTAAATCACATAAAACA-ATATTTATTCAAATCA
1 AATTAAAT-A-A-AAAATATATATTT-TTCGAATCA
*
1649046 AATTAAAATAAAAAATATATAATTTTCG
1 AATT-AAATAAAAAATATATATTTTTCG
1649074 GTTCGTGACA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
32 8 0.15
33 9 0.17
34 13 0.25
35 18 0.35
36 4 0.08
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (32 bp):
AATTAAATAAAAAATATATATTTTTCGAATCA
Found at i:1649831 original size:119 final size:120
Alignment explanation
Indices: 1649616--1649833 Score: 266
Period size: 119 Copynumber: 1.8 Consensus size: 120
1649606 TGTTGATTTG
* * * *
1649616 AATGTGTTGTGATATCGATTTTGTGTATTTTTTGTGAAATCCCTAATTTTTATATCCCTGATTTG
1 AATGTGTTGTGATATCGATTTTGTGTATTCTTTGTGAAAGCCCTAATTCTTATATACCTGATTTG
* *
1649681 TTAAACCCTAAACTTGAAACGCAATCGATAAAATTAGTCGTATTCTGATGCTTTA
66 TAAAACCCTAAACTTGAAACGCAATCAATAAAATTAGTCGTATTCTGATGCTTTA
* * *
1649736 AATGTGTTGTGGTATCTG-TTTTGTG-CTTCTTTGTGAAAGCCCTAATTCTTAGT-TACTTG-TT
1 AATGTGTTGTGATATC-GATTTTGTGTATTCTTTGTGAAAGCCCTAATTCTTA-TATACCTGATT
* *
1649797 TGATAAAACCCTAAATTTGAAA-GACATTCAATAAAAT
64 TG-TAAAACCCTAAACTTGAAACG-CAATCAATAAAAT
1649834 GTGTAAAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
118 5 0.06
119 54 0.65
120 23 0.28
121 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.42
Consensus pattern (120 bp):
AATGTGTTGTGATATCGATTTTGTGTATTCTTTGTGAAAGCCCTAATTCTTATATACCTGATTTG
TAAAACCCTAAACTTGAAACGCAATCAATAAAATTAGTCGTATTCTGATGCTTTA
Found at i:1653395 original size:14 final size:15
Alignment explanation
Indices: 1653364--1653393 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1653354 TCACGCTGGG
*
1653364 ATTTTTTTTAATAAA
1 ATTTTTTTAAATAAA
1653379 ATTTTTTTAAATAAA
1 ATTTTTTTAAATAAA
1653394 TTCTCAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTTTTAAATAAA
Found at i:1657665 original size:30 final size:30
Alignment explanation
Indices: 1657629--1657695 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
1657619 AGGTGGGTTT
1657629 ATTCTTCGTAAGTAATTAAGCTAGGCTTTC
1 ATTCTTCGTAAGTAATTAAGCTAGGCTTTC
*
1657659 ATTCTTCGTTAGTAATTAAGCTAGGCTTTC
1 ATTCTTCGTAAGTAATTAAGCTAGGCTTTC
1657689 ATTCTTC
1 ATTCTTC
1657696 CTTTTTTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (30 bp):
ATTCTTCGTAAGTAATTAAGCTAGGCTTTC
Found at i:1659827 original size:16 final size:16
Alignment explanation
Indices: 1659806--1659838 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1659796 GAACGTGATA
1659806 TCACACTAATAAGAGC
1 TCACACTAATAAGAGC
1659822 TCACACTAATAAGAGC
1 TCACACTAATAAGAGC
1659838 T
1 T
1659839 GATAGTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.21
Consensus pattern (16 bp):
TCACACTAATAAGAGC
Found at i:1664957 original size:29 final size:30
Alignment explanation
Indices: 1664907--1664987 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
1664897 TTCGTGTTCA
* * *
1664907 TTTATTTATTTTCGAAAGTGTTTGTGTTTG
1 TTTATTTATTTTTGAAAGTGTTTGTATTCG
* *
1664937 TTTATTT-TTTTTTAACGTGTTTGTATTCG
1 TTTATTTATTTTTGAAAGTGTTTGTATTCG
*
1664966 TTTGTTTATTTTTGAAAGTGTT
1 TTTATTTATTTTTGAAAGTGTT
1664988 CAATTCGTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 23 0.55
30 19 0.45
ACGTcount: A:0.16, C:0.04, G:0.17, T:0.63
Consensus pattern (30 bp):
TTTATTTATTTTTGAAAGTGTTTGTATTCG
Found at i:1665086 original size:23 final size:23
Alignment explanation
Indices: 1665057--1665105 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1665047 TATTTGTCAG
* *
1665057 CATGTTCGTTAGGAGTTCGCAAA
1 CATGTTCGTCAAGAGTTCGCAAA
*
1665080 CATGTTCGTCAAGAGTTTGCAAA
1 CATGTTCGTCAAGAGTTCGCAAA
1665103 CAT
1 CAT
1665106 ATTTGTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (23 bp):
CATGTTCGTCAAGAGTTCGCAAA
Found at i:1671645 original size:31 final size:31
Alignment explanation
Indices: 1671610--1671674 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1671600 AGGGGAAATG
*
1671610 GTCCCTAACATTATCAATCCATTCGATTTTA
1 GTCCCTAACATTATCAATCCATTCGAATTTA
* * *
1671641 GTCCCTAATATTATCGATCCATTTGAATTTA
1 GTCCCTAACATTATCAATCCATTCGAATTTA
1671672 GTC
1 GTC
1671675 TCTCGACCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (31 bp):
GTCCCTAACATTATCAATCCATTCGAATTTA
Found at i:1685409 original size:31 final size:30
Alignment explanation
Indices: 1685359--1685442 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 30
1685349 GATAGATAGA
*
1685359 TTTAATTGACTCTTTTTAAAAAAAATTAAAGG
1 TTTAATTGAAT-TTTTTAAAAAAAATTAAA-G
**
1685391 TTTAATTGAATTTTTTAAAAAAGTTTAAAG
1 TTTAATTGAATTTTTTAAAAAAAATTAAAG
* * *
1685421 TTT-ATTTATTTTTTTAAGAAAA
1 TTTAATTGAATTTTTTAAAAAAA
1685443 TAAAAATTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.33
30 4 0.09
31 16 0.36
32 10 0.22
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (30 bp):
TTTAATTGAATTTTTTAAAAAAAATTAAAG
Found at i:1685411 original size:30 final size:29
Alignment explanation
Indices: 1685359--1685443 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 29
1685349 GATAGATAGA
*
1685359 TTTAATTGACTCTTTTTAAAAAAAATTAAAGG
1 TTTAATTGAAT-TTTTT-AAAAAAATTAAA-G
*
1685391 TTTAATTGAATTTTTTAAAAAAGTTTAAAG
1 TTTAATTGAATTTTTTAAAAAA-ATTAAAG
* * *
1685421 TTT-ATTTATTTTTTTAAGAAAAT
1 TTTAATTGAATTTTTTAAAAAAAT
1685444 AAAAATTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
28 1 0.02
29 15 0.33
30 10 0.22
31 10 0.22
32 10 0.22
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.48
Consensus pattern (29 bp):
TTTAATTGAATTTTTTAAAAAAATTAAAG
Found at i:1686359 original size:15 final size:16
Alignment explanation
Indices: 1686339--1686407 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 16
1686329 TAATTGGATG
1686339 AAATAAATATA-AAAA
1 AAATAAATATACAAAA
1686354 AAATAAAATTGAATA-AAATA
1 AAAT-AAA-T--ATACAAA-A
* *
1686374 AAATAAATAAAGAAAA
1 AAATAAATATACAAAA
*
1686390 AAATATATATACAAAA
1 AAATAAATATACAAAA
1686406 AA
1 AA
1686408 GAATAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
15 4 0.09
16 21 0.48
17 4 0.09
18 1 0.02
19 9 0.20
20 5 0.11
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.20
Consensus pattern (16 bp):
AAATAAATATACAAAA
Found at i:1686373 original size:5 final size:5
Alignment explanation
Indices: 1686339--1686384 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
1686329 TAATTGGATG
* *
1686339 AAATA AATATA AAA-A AAATA AAATT GAATA AAATA AAAT- AAATA AA
1 AAATA AA-ATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
1686385 GAAAAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
4 8 0.24
5 21 0.62
6 5 0.15
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:1686496 original size:13 final size:13
Alignment explanation
Indices: 1686480--1686535 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
1686470 CATAATGAAA
*
1686480 ATAAATAAATAGT
1 ATAAATAAATAAT
1686493 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
*
1686507 A-AAATAAAAAAT
1 ATAAATAAATAAT
*
1686519 ATATATAAA-AAT
1 ATAAATAAATAAT
1686531 ATAAA
1 ATAAA
1686536 AATATATGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 14 0.38
13 16 0.43
14 7 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:1686500 original size:26 final size:25
Alignment explanation
Indices: 1686471--1686589 Score: 81
Period size: 26 Copynumber: 4.7 Consensus size: 25
1686461 AACTAAAAAC
1686471 ATAATGAAAATAAATAAATAGTATAA
1 ATAAT-AAAATAAATAAATAGTATAA
* * *
1686497 ATAA-AATAATAAAATAAAAAATATAT
1 ATAATAA-AAT-AAATAAATAGTATAA
1686523 ATAA-AAATATAAA-AATATATGTATAA
1 ATAATAAA-ATAAATAA-ATA-GTATAA
*
1686549 TATAATAAAAT-ATTAAATAGTA-ACA
1 -ATAATAAAATAAATAAATAGTATA-A
1686574 ATAAT--AATAAATAAAT
1 ATAATAAAATAAATAAAT
1686590 GAAAAATAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 23
0.71 0.08 0.22
Matches are distributed among these distances:
22 3 0.04
23 6 0.08
24 10 0.13
25 13 0.17
26 32 0.43
27 8 0.11
28 3 0.04
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (25 bp):
ATAATAAAATAAATAAATAGTATAA
Found at i:1686531 original size:19 final size:20
Alignment explanation
Indices: 1686505--1686561 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1686495 AAATAAAATA
1686505 ATAAAATAAAAAATATATAT
1 ATAAAATAAAAAATATATAT
*
1686525 A-AAAATATAAAAATATATGT
1 ATAAAATA-AAAAATATATAT
*
1686545 ATAATATAATAAAATAT
1 ATAAAATAA-AAAATAT
1686562 TAAATAGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.19
20 14 0.44
21 12 0.38
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
ATAAAATAAAAAATATATAT
Found at i:1686560 original size:21 final size:21
Alignment explanation
Indices: 1686502--1686612 Score: 77
Period size: 21 Copynumber: 5.3 Consensus size: 21
1686492 TATAAATAAA
*
1686502 ATAATAAAATAAAAAATATAT
1 ATAATAAAATAAAATATATAT
*
1686523 ATAA-AAATATAAAAATATATGT
1 ATAATAAA-AT-AAAATATATAT
* *
1686545 ATAATATAATAAAATAT-TAA
1 ATAATAAAATAAAATATATAT
* * *
1686565 ATAGTAACAATAATAATAAATAA
1 ATAATAA-AATAA-AATATATAT
* *
1686588 ATGA-AAAAT-AAATATACAT
1 ATAATAAAATAAAATATATAT
1686607 ATAATA
1 ATAATA
1686613 TTAACTAAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 15
0.70 0.14 0.15
Matches are distributed among these distances:
19 9 0.13
20 11 0.16
21 21 0.30
22 21 0.30
23 7 0.10
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (21 bp):
ATAATAAAATAAAATATATAT
Found at i:1686778 original size:25 final size:25
Alignment explanation
Indices: 1686732--1686782 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1686722 TAGATAAAAA
* *
1686732 AATAATAATATAATATATATATAAT
1 AATAATAATAGAAAATATATATAAT
1686757 AATAATAATAGGAAAATA-ATATAAT
1 AATAATAATA-GAAAATATATATAAT
1686782 A
1 A
1686783 TAACTCAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (25 bp):
AATAATAATAGAAAATATATATAAT
Found at i:1687335 original size:37 final size:37
Alignment explanation
Indices: 1687250--1687343 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
1687240 GGATCCTATC
* ** * *
1687250 TTTAGGAGTTTAAATAATAGTAAAACTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGCAAAACTCTATCATATT
*
1687287 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGCAAAACTCTATCATATT
1687324 TTTAGGAGTTTGAATCCTAG
1 TTTAGGAGTTTGAATCCTAG
1687344 TAGGACGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGCAAAACTCTATCATATT
Found at i:1687871 original size:23 final size:23
Alignment explanation
Indices: 1687793--1687873 Score: 58
Period size: 23 Copynumber: 3.5 Consensus size: 23
1687783 TATTTATGTT
** * *
1687793 TATTTGTTTTTCGTTCACGAATA
1 TATTTGTTTAACGTTCGCGAAAA
* *
1687816 TGTTTGTTTAAC-TATTGC-AAACA
1 TATTTGTTTAACGT-TCGCGAAA-A
* *
1687839 TGTTTATTTAACGTTCGCGAAAA
1 TATTTGTTTAACGTTCGCGAAAA
1687862 TATTTGTTTAAC
1 TATTTGTTTAAC
1687874 ATTTGTTTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
22 3 0.07
23 37 0.84
24 4 0.09
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (23 bp):
TATTTGTTTAACGTTCGCGAAAA
Found at i:1689145 original size:11 final size:11
Alignment explanation
Indices: 1689110--1689153 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
1689100 TACCATATTG
*
1689110 AATTTTATTTTA
1 AATTTT-TTTTT
*
1689122 AACTTTCTTTTT
1 AA-TTTTTTTTT
1689134 AATTTTTTTTT
1 AATTTTTTTTT
1689145 AATTTTTTT
1 AATTTTTTT
1689154 ATTTATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 17 0.61
12 8 0.29
13 3 0.11
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (11 bp):
AATTTTTTTTT
Found at i:1689158 original size:24 final size:25
Alignment explanation
Indices: 1689105--1689169 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
1689095 GATTTTACCA
*
1689105 TATTGAATTTTATTTTAAACTTTCT
1 TATTTAATTTTATTTTAAACTTTCT
* * *
1689130 T-TTTAATTTT-TTTTTAATTTTTT
1 TATTTAATTTTATTTTAAACTTTCT
1689153 TATTTATATTTATATTT
1 TATTTA-ATTT-TATTT
1689170 CTTTTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 11 0.34
24 12 0.38
25 5 0.16
26 1 0.03
27 3 0.09
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.71
Consensus pattern (25 bp):
TATTTAATTTTATTTTAAACTTTCT
Found at i:1689169 original size:20 final size:20
Alignment explanation
Indices: 1689137--1689185 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1689127 TCTTTTTAAT
*
1689137 TTTTTTTTA-ATTT-TTTTA
1 TTTTATTTATATTTCTTTTA
1689155 TTTATATTTATATTTCTTTTA
1 TTT-TATTTATATTTCTTTTA
1689176 TTTTATTTAT
1 TTTTATTTAT
1689186 CTTCATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 5 0.19
20 11 0.41
21 8 0.30
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTATTTATATTTCTTTTA
Found at i:1689410 original size:12 final size:12
Alignment explanation
Indices: 1689393--1689448 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
1689383 GTAAATGAAT
1689393 TTATAAACGAG-
1 TTATAAACGAGA
*
1689404 TTGATAAACAAGA
1 TT-ATAAACGAGA
1689417 TTATAAACGAGA
1 TTATAAACGAGA
* * * *
1689429 CTATATATGAGC
1 TTATAAACGAGA
1689441 TTATAAAC
1 TTATAAAC
1689449 AGAGTTAAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
11 2 0.06
12 30 0.88
13 2 0.06
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (12 bp):
TTATAAACGAGA
Found at i:1696600 original size:10 final size:10
Alignment explanation
Indices: 1696585--1696641 Score: 80
Period size: 10 Copynumber: 5.7 Consensus size: 10
1696575 TATCTTGTAA
*
1696585 TTTAATATAC
1 TTTAATCTAC
1696595 TTTAATCTAC
1 TTTAATCTAC
1696605 TTTAATCTGA-
1 TTTAATCT-AC
1696615 TTTAATCTAC
1 TTTAATCTAC
*
1696625 TTTAATCTAA
1 TTTAATCTAC
1696635 TTTAATC
1 TTTAATC
1696642 ATTTAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
9 1 0.02
10 41 0.95
11 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (10 bp):
TTTAATCTAC
Found at i:1696618 original size:30 final size:30
Alignment explanation
Indices: 1696584--1696641 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1696574 CTATCTTGTA
*
1696584 ATTTAATATACTTTAATCTACTTTAATCTG
1 ATTTAATATACTTTAATCTAATTTAATCTG
*
1696614 ATTTAATCTACTTTAATCTAATTTAATC
1 ATTTAATATACTTTAATCTAATTTAATC
1696642 ATTTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.50
Consensus pattern (30 bp):
ATTTAATATACTTTAATCTAATTTAATCTG
Found at i:1697967 original size:19 final size:18
Alignment explanation
Indices: 1697932--1697966 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1697922 TTGATTCAAT
1697932 AATTTAAAAATATATATA
1 AATTTAAAAATATATATA
*
1697950 AATTTTAAAATAT-TATA
1 AATTTAAAAATATATATA
1697967 TTGGGAAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTTAAAAATATATATA
Found at i:1701567 original size:20 final size:21
Alignment explanation
Indices: 1701542--1701584 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1701532 AATATGAACT
*
1701542 ATGTCTT-AAATACATTATAA
1 ATGTCTTCAAATACAATATAA
*
1701562 ATGTCTTCAAATATAATATAA
1 ATGTCTTCAAATACAATATAA
1701583 AT
1 AT
1701585 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (21 bp):
ATGTCTTCAAATACAATATAA
Found at i:1701676 original size:7 final size:7
Alignment explanation
Indices: 1701664--1701777 Score: 228
Period size: 7 Copynumber: 16.3 Consensus size: 7
1701654 AAACTGACGA
1701664 GGAGAAG
1 GGAGAAG
1701671 GGAGAAG
1 GGAGAAG
1701678 GGAGAAG
1 GGAGAAG
1701685 GGAGAAG
1 GGAGAAG
1701692 GGAGAAG
1 GGAGAAG
1701699 GGAGAAG
1 GGAGAAG
1701706 GGAGAAG
1 GGAGAAG
1701713 GGAGAAG
1 GGAGAAG
1701720 GGAGAAG
1 GGAGAAG
1701727 GGAGAAG
1 GGAGAAG
1701734 GGAGAAG
1 GGAGAAG
1701741 GGAGAAG
1 GGAGAAG
1701748 GGAGAAG
1 GGAGAAG
1701755 GGAGAAG
1 GGAGAAG
1701762 GGAGAAG
1 GGAGAAG
1701769 GGAGAAG
1 GGAGAAG
1701776 GG
1 GG
1701778 CAACAATTGG
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 107 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (7 bp):
GGAGAAG
Found at i:1707702 original size:20 final size:21
Alignment explanation
Indices: 1707664--1707702 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1707654 AAATGAGATA
* *
1707664 AAAAATAAAAGAAGTAAAAGT
1 AAAAATAAAACAAGAAAAAGT
1707685 AAAAAT-AAACAAGAAAAA
1 AAAAATAAAACAAGAAAAA
1707703 AATGACGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAAATAAAACAAGAAAAAGT
Found at i:1707928 original size:2 final size:2
Alignment explanation
Indices: 1707921--1707961 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1707911 AGTTATATGA
1707921 AT AT AT AT AT 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 AT AT AT AT AT A
1707962 ACAACTTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1708094 original size:35 final size:32
Alignment explanation
Indices: 1707983--1708095 Score: 97
Period size: 35 Copynumber: 3.4 Consensus size: 32
1707973 ACAAGGTATA
*
1707983 AAAAAATAATAGTAATAAT-AAGTAT-TAAAAT
1 AAAAAATAA-AGTAATAATAAATTATATAAAAT
* * *
1708014 AAAAAA-ATAGTAATAAAAAAATTATAAAAAAT
1 AAAAAATAAAGTAAT-AATAAATTATATAAAAT
*
1708046 ATGAAAATCAAAGTAATATATAAATATATATATAAAT
1 A-AAAAAT-AAAGTAATA-ATAAAT-TATATA-AAAT
1708083 AAAAAATAAAGTA
1 AAAAAATAAAGTA
1708096 TAAATGAAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
29 6 0.09
30 3 0.05
31 11 0.17
32 6 0.09
33 4 0.06
34 1 0.02
35 18 0.28
36 10 0.16
37 5 0.08
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (32 bp):
AAAAAATAAAGTAATAATAAATTATATAAAAT
Found at i:1708669 original size:35 final size:35
Alignment explanation
Indices: 1708600--1708670 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
1708590 TAAAAAATCT
* * * *
1708600 TATTTTAGACTAGTATTTGAGTCCTGATCCAACTC
1 TATTCTAGACTAGTATTTAAGTCATAATCCAACTC
*
1708635 TATTCTAGACTAGTATTTAAGTCATAATCTAACTC
1 TATTCTAGACTAGTATTTAAGTCATAATCCAACTC
1708670 T
1 T
1708671 TCTTTATTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (35 bp):
TATTCTAGACTAGTATTTAAGTCATAATCCAACTC
Found at i:1710203 original size:17 final size:19
Alignment explanation
Indices: 1710183--1710222 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
1710173 AATTACTCTA
1710183 ATTTTTAAA-AATA-TTTT
1 ATTTTTAAATAATATTTTT
*
1710200 ATTTTTAAATTATATTTTT
1 ATTTTTAAATAATATTTTT
1710219 ATTT
1 ATTT
1710223 GATACTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 3 0.15
19 8 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTAAATAATATTTTT
Found at i:1713944 original size:23 final size:23
Alignment explanation
Indices: 1713918--1713978 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1713908 CTCGTATAAA
*
1713918 TGCACCTAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1713941 TGCATCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1713964 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
1713979 TATAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1723890 original size:21 final size:21
Alignment explanation
Indices: 1723864--1723905 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1723854 ATTCAATCAG
1723864 GTATGCATTTAGGTTTTCTTT
1 GTATGCATTTAGGTTTTCTTT
1723885 GTATGCATTTAGGTTTTCTTT
1 GTATGCATTTAGGTTTTCTTT
1723906 CTCTACTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.19, T:0.57
Consensus pattern (21 bp):
GTATGCATTTAGGTTTTCTTT
Found at i:1725104 original size:193 final size:196
Alignment explanation
Indices: 1724737--1725128 Score: 729
Period size: 193 Copynumber: 2.0 Consensus size: 196
1724727 ATAATTTCTG
1724737 ATACAGGTGAATGAATCAGATGAAGTGCTGGTCAAGTCATCATTTCTTGCTGAACTTCAGCGCCG
1 ATACAGGTGAATGAATCAGATGAAGTGCTGGTCAAG--ATCATTTCTTGCTGAACTTCAGCGCCG
1724802 AGTTCTTAAAGCTGAGGCTGTTCTGAGGGAGAAAGAAGAGAAAACGACATCCTCCACCAGCGACT
64 AGTTCTTAAAGCTGAGGCTGTTCTGAGGGAGAAAGAAGAGAAAACGACATCCTCCACCAGCGACT
1724867 CCTACAATATGAGAACCGTTGGTCTGAATATGAGCTAAAAATGAAGTCCATGG-AGAAGTGTGGC
129 CCTACAATATGAGAACCGTTGGTCTGAATATGAGCTAAAAATGAAGTCCATGGAAGAAGTGTGGC
1724931 AGA
194 AGA
1724934 ATACAGGTGAATGAATCAGATGAA-TGCTGGTC-AG-TCATTTCTTGCTGAACTTCAGCGCCGAG
1 ATACAGGTGAATGAATCAGATGAAGTGCTGGTCAAGATCATTTCTTGCTGAACTTCAGCGCCGAG
1724996 TTCTTAAAGCTGAGGCTGTTCTGAGGGAGAAAGAAGAGAAAAACGACATCCTCCACCAGCGACTC
66 TTCTTAAAGCTGAGGCTGTTCTGAGGGAGAAAGAAGAG-AAAACGACATCCTCCACCAGCGACTC
1725061 CTACAATATGAGAACCGTTGGTCTGAATATGAGCTAAAAATGAAGTCCATGGAAGAAGTGTGGCA
130 CTACAATATGAGAACCGTTGGTCTGAATATGAGCTAAAAATGAAGTCCATGGAAGAAGTGTGGCA
1725126 GA
195 GA
1725128 A
1 A
1725129 ACAAATGAGG
Statistics
Matches: 193, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
192 66 0.34
193 78 0.40
194 15 0.08
195 2 0.01
196 8 0.04
197 24 0.12
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (196 bp):
ATACAGGTGAATGAATCAGATGAAGTGCTGGTCAAGATCATTTCTTGCTGAACTTCAGCGCCGAG
TTCTTAAAGCTGAGGCTGTTCTGAGGGAGAAAGAAGAGAAAACGACATCCTCCACCAGCGACTCC
TACAATATGAGAACCGTTGGTCTGAATATGAGCTAAAAATGAAGTCCATGGAAGAAGTGTGGCAG
A
Found at i:1732927 original size:16 final size:18
Alignment explanation
Indices: 1732895--1732928 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1732885 AGTTTAAATT
1732895 TAAATTTATTGATTGTTG
1 TAAATTTATTGATTGTTG
1732913 TAAA-TTATT-ATTGTTG
1 TAAATTTATTGATTGTTG
1732929 CATAAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (18 bp):
TAAATTTATTGATTGTTG
Found at i:1739066 original size:18 final size:18
Alignment explanation
Indices: 1739043--1739113 Score: 97
Period size: 18 Copynumber: 3.8 Consensus size: 18
1739033 AGGGATTATC
1739043 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
1739061 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
1739080 CAGTGGTCCTTCGGGATAT
1 -AGTGGTCCTTCGGGACAT
1739099 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
1739114 AAATATTCAG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 29 0.63
19 4 0.09
20 13 0.28
ACGTcount: A:0.18, C:0.20, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1739125 original size:23 final size:19
Alignment explanation
Indices: 1739034--1739113 Score: 92
Period size: 18 Copynumber: 4.2 Consensus size: 19
1739024 CAAGAGTCGA
1739034 GGGATTATCAGTGGTCCTTC
1 GGGA-TATCAGTGGTCCTTC
* *
1739054 GGGACAT-AGTGGTTCTTC
1 GGGATATCAGTGGTCCTTC
* *
1739072 GGAACAATCAGTGGTCCTTC
1 GGGA-TATCAGTGGTCCTTC
1739092 GGGATAT-AGTGGTCCTTC
1 GGGATATCAGTGGTCCTTC
1739110 GGGA
1 GGGA
1739114 AAATATTCAG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
18 28 0.55
19 6 0.12
20 17 0.33
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.30
Consensus pattern (19 bp):
GGGATATCAGTGGTCCTTC
Found at i:1754972 original size:2 final size:2
Alignment explanation
Indices: 1754965--1754996 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1754955 TTTAGGGTGG
1754965 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
1754997 TACTAACACA
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:1755882 original size:3 final size:3
Alignment explanation
Indices: 1755874--1755903 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1755864 ACACCCCTCG
1755874 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1755904 TTTCTTTCTT
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):
ATT
Found at i:1758070 original size:3 final size:3
Alignment explanation
Indices: 1758062--1758086 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1758052 TAGATCATAT
1758062 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
1758087 AACCCAACAT
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:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1777731 original size:21 final size:21
Alignment explanation
Indices: 1777707--1777757 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1777697 ACTTCGACTA
*
1777707 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
1777728 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
1777749 TCGCGTTGC
1 TCGCGTTGC
1777758 AAATCTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:1780156 original size:26 final size:24
Alignment explanation
Indices: 1780109--1780156 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
1780099 TCAAATTCGG
*
1780109 TTGCGGATTTTGTTACGAATGTGA
1 TTGCGGATTGTGTTACGAATGTGA
*
1780133 TTGCGGTATTGTGATTACGGATGT
1 TTGCGG-ATTGTG-TTACGAATGT
1780157 TGCGGACGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 5 0.25
26 9 0.45
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (24 bp):
TTGCGGATTGTGTTACGAATGTGA
Found at i:1780562 original size:31 final size:31
Alignment explanation
Indices: 1780524--1780584 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1780514 AGTTACGTCG
**
1780524 GGGACCATATTACAAATTGACTAAATGTTGA
1 GGGACCATATTACAAACGGACTAAATGTTGA
* *
1780555 GGGACCATATTGCAAACGGATTAAATGTTG
1 GGGACCATATTACAAACGGACTAAATGTTG
1780585 GGAGATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (31 bp):
GGGACCATATTACAAACGGACTAAATGTTGA
Found at i:1781043 original size:26 final size:26
Alignment explanation
Indices: 1780988--1781043 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
1780978 ATAACATCGA
* * *
1780988 AATTCAATTTTTTAATCTTATTTAAG
1 AATTCAATATTTTAATCTTATTAAAC
*
1781014 AATTTAATATTTT-ATCTTATTGAAAC
1 AATTCAATATTTTAATCTTATT-AAAC
1781040 AATT
1 AATT
1781044 AGTATGGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.52
Consensus pattern (26 bp):
AATTCAATATTTTAATCTTATTAAAC
Found at i:1781763 original size:10 final size:10
Alignment explanation
Indices: 1781744--1781775 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1781734 TTTATTATTC
1781744 TCAC-CTCTT
1 TCACACTCTT
1781753 TCACACTCTT
1 TCACACTCTT
1781763 TCACACTCTT
1 TCACACTCTT
1781773 TCA
1 TCA
1781776 ACTTCAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (10 bp):
TCACACTCTT
Found at i:1782684 original size:30 final size:31
Alignment explanation
Indices: 1782648--1782707 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
1782638 ATACAATCTC
1782648 CAACATTTAGTCCG-TTGCAATATGGTCCCT
1 CAACATTTAGTCCGTTTGCAATATGGTCCCT
1782678 CAACATTTAGTCCGTTTGCAATATGGTCCC
1 CAACATTTAGTCCGTTTGCAATATGGTCCC
1782708 CGACGTAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 14 0.48
31 15 0.52
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (31 bp):
CAACATTTAGTCCGTTTGCAATATGGTCCCT
Found at i:1783075 original size:16 final size:17
Alignment explanation
Indices: 1783048--1783083 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1783038 GATATGAGAA
1783048 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
1783065 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
1783081 AAA
1 AAA
1783084 ATAGCGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:1785723 original size:23 final size:23
Alignment explanation
Indices: 1785697--1785748 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1785687 AACGCCAGCT
1785697 AACAACTTCTTTAAATAACTAGC
1 AACAACTTCTTTAAATAACTAGC
* *
1785720 AACAGCTTCTTTAACTAACTAGC
1 AACAACTTCTTTAAATAACTAGC
1785743 AACAAC
1 AACAAC
1785749 ACTCTTAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (23 bp):
AACAACTTCTTTAAATAACTAGC
Found at i:1785756 original size:23 final size:23
Alignment explanation
Indices: 1785697--1785761 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
1785687 AACGCCAGCT
* *
1785697 AACAACTTCTTTAAATAACTAGC
1 AACAACCTCTTTAACTAACTAGC
* *
1785720 AACAGCTTCTTTAACTAACTAGC
1 AACAACCTCTTTAACTAACTAGC
1785743 AACAACACTC-TTAAC-AACT
1 AACAAC-CTCTTTAACTAACT
1785762 TTAGTTACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 4 0.11
23 31 0.84
24 2 0.05
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.28
Consensus pattern (23 bp):
AACAACCTCTTTAACTAACTAGC
Found at i:1788957 original size:23 final size:23
Alignment explanation
Indices: 1788931--1788998 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1788921 ATTATTATAT
1788931 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
1788954 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
1788977 GGCACGTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1788999 AGTTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1792590 original size:21 final size:21
Alignment explanation
Indices: 1792565--1792605 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1792555 TCTGGGCAAA
* *
1792565 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
1792586 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
1792606 ACGAACAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:1794091 original size:23 final size:23
Alignment explanation
Indices: 1794023--1794091 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1794013 CATTATTATA
* *
1794023 TGGCACTTCAGTACATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
1794046 CGGTACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
1794069 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
1794092 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1795801 original size:27 final size:27
Alignment explanation
Indices: 1795747--1795812 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
1795737 TCAACATCAT
***
1795747 TCCCAGG-GGATGATTCTTCAGTTCCAC
1 TCCCAGGTGG-TGATTCTTCAGCAACAC
1795774 TCCCAGGTGGTGATTCTTCAGCAACAC
1 TCCCAGGTGGTGATTCTTCAGCAACAC
1795801 TCCCAGGTGGTG
1 TCCCAGGTGGTG
1795813 TAGAGTGCGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.27
Consensus pattern (27 bp):
TCCCAGGTGGTGATTCTTCAGCAACAC
Found at i:1796932 original size:23 final size:23
Alignment explanation
Indices: 1796885--1796935 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
1796875 AGCTGGTAAT
1796885 ATTAAAAATTTCAGAGGTTCTGAA
1 ATTAAAAATTTCA-AGGTTCTGAA
1796909 ATTATAAAATTTC-AGGTTGC-GAA
1 ATTA-AAAATTTCAAGGTT-CTGAA
1796932 ATTA
1 ATTA
1796936 GATTATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 12 0.48
24 5 0.20
25 8 0.32
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (23 bp):
ATTAAAAATTTCAAGGTTCTGAA
Found at i:1799454 original size:27 final size:29
Alignment explanation
Indices: 1799416--1799469 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
1799406 TTAATTCATC
*
1799416 TCTTAAAATTTAGAT-A-TATTAATTTTA
1 TCTTAAAATTTACATAATTATTAATTTTA
*
1799443 TCTTAAATTTTACATAATTATTAATTT
1 TCTTAAAATTTACATAATTATTAATTT
1799470 AATTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 13 0.57
28 1 0.04
29 9 0.39
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (29 bp):
TCTTAAAATTTACATAATTATTAATTTTA
Found at i:1799512 original size:34 final size:34
Alignment explanation
Indices: 1799447--1799513 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
1799437 ATTTTATCTT
* * *
1799447 AAATTTTACATAATTATTAATTTAATTTTTAAAC
1 AAATTTTAAATAAGTATTAACTTAATTTTTAAAC
*
1799481 AAATTTTAAATAAGTATTAGCTT-ATTATTTAAA
1 AAATTTTAAATAAGTATTAACTTAATT-TTTAAA
1799514 TTTTGTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 3 0.11
34 25 0.89
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (34 bp):
AAATTTTAAATAAGTATTAACTTAATTTTTAAAC
Found at i:1820134 original size:10 final size:10
Alignment explanation
Indices: 1820119--1820145 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1820109 GGAGAAAGAA
1820119 ATGATTTGGG
1 ATGATTTGGG
1820129 ATGATTTGGG
1 ATGATTTGGG
1820139 ATGATTT
1 ATGATTT
1820146 TGAAGCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (10 bp):
ATGATTTGGG
Found at i:1824867 original size:163 final size:162
Alignment explanation
Indices: 1824594--1824917 Score: 544
Period size: 163 Copynumber: 2.0 Consensus size: 162
1824584 AAGTGTTTAC
*
1824594 AAAACACTCACTACTCACAAGAAAACTTCTAGTATTGGGAGAAAGAAATGATTTGTGATGATTTG
1 AAAACACTCACTACTCACAAGAAAACTTCTAGTATTGAGAGAAAGAAATGATTTGTGATGATTTG
* *
1824659 AAGGTAAATGGGTTAGGGTATTTATAGTTGAAGCTTAGAGACTAATCTTGTAAATACCCTAAAGT
66 AAGGTAAATGGGTTAGGGTATTTATAGTTGAAGCTTAGAGACTAATCTTATAAATACCCTAAAAT
*
1824724 ATGTAGGGACTAAAGTGTAATTAACCCTATTA
131 ATATAGGGACTAAAGTGTAATTAACCCTATTA
*
1824756 AAAACACTCACTACTCACAAG-AAAGTTCTTTAGTATTGAGAGAAAGAAATGATTTG-GCATGAT
1 AAAACACTCACTACTCACAAGAAAACTTC--TAGTATTGAGAGAAAGAAATGATTTGTG-ATGAT
* *
1824819 TTGAATGTAAATGGGTTAGGGTATTTATAGTTGAAGCTTAGGGACTAATCTTATAAATACCCTAA
63 TTGAAGGTAAATGGGTTAGGGTATTTATAGTTGAAGCTTAGAGACTAATCTTATAAATACCCTAA
1824884 AATATATAGGGACTAAAGTGTAATTAACCCTATT
128 AATATATAGGGACTAAAGTGTAATTAACCCTATT
1824918 GTAATTGTAA
Statistics
Matches: 152, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
161 6 0.04
162 22 0.14
163 124 0.82
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (162 bp):
AAAACACTCACTACTCACAAGAAAACTTCTAGTATTGAGAGAAAGAAATGATTTGTGATGATTTG
AAGGTAAATGGGTTAGGGTATTTATAGTTGAAGCTTAGAGACTAATCTTATAAATACCCTAAAAT
ATATAGGGACTAAAGTGTAATTAACCCTATTA
Found at i:1825792 original size:259 final size:259
Alignment explanation
Indices: 1825333--1826115 Score: 1417
Period size: 259 Copynumber: 3.0 Consensus size: 259
1825323 AAGGAACTGC
* *
1825333 AATCATTCTGCTGCTCAAAATGAATGCAATTTTCCACCACTCATAGGCTTTCCTAGTGC-GAACC
1 AATCATTATGCTGCTCAAAATGAATGCAATTTTCCACCGCTCATAGGCTTTCCTAGTGCGGAA-C
1825397 CAATGGCATATGATTGATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTA
65 CAATGGCATATGATTGATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTA
* * *
1825462 CTGTTGTACACCCATAACTAATAGAGATTGTAGTTTTCAAATTTCAATTACAATAATGCTCTTAA
130 CTGTTGCACACCCATAACTGATAGAGATTGTAGTTTTCAAATTTCAATTACAATAAAGCTCTTAA
1825527 CATCATACTATATCGTATTGTGATTGATAATATCACCATACTTTCTATTTTACTGTTTAGTTAGA
195 CATCATACTATATCGTATTGTGATTGATAATATCACCATACTTTCTATTTTACTGTTTAGTTAGA
1825592 AATCATTATGCTGCTCAAAATGAATGCAATTTTCCACCGCTCATAGGCTTTCCTAGTGCGGAACC
1 AATCATTATGCTGCTCAAAATGAATGCAATTTTCCACCGCTCATAGGCTTTCCTAGTGCGGAACC
* *
1825657 AATGGCATATGATTAATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTAT
66 AATGGCATATGATTGATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTAC
1825722 TGTTGCACACCCATAACTGATAGAGATTGTAGTTTTCAAATTTCAATTACAATAAAGCTCTTAAC
131 TGTTGCACACCCATAACTGATAGAGATTGTAGTTTTCAAATTTCAATTACAATAAAGCTCTTAAC
* *
1825787 ATCATACTATATCATATTGTGATTGATAATATCACCATACTTTCTATTTTAGTGTTTAGTTAGA
196 ATCATACTATATCGTATTGTGATTGATAATATCACCATACTTTCTATTTTACTGTTTAGTTAGA
1825851 AATCATTATGCTGCTCAAAATGAATGCAATTTTCCACCGCTCATAGGCTTTCCTAGTGCGGAACC
1 AATCATTATGCTGCTCAAAATGAATGCAATTTTCCACCGCTCATAGGCTTTCCTAGTGCGGAACC
1825916 AATGGCATATGATTGATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTAC
66 AATGGCATATGATTGATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTAC
*
1825981 TG-TGCACACCCATAATTGATAGAGATTGTAGTTTTCAAATTTCAATTACAATAAAGCTCTTAAC
131 TGTTGCACACCCATAACTGATAGAGATTGTAGTTTTCAAATTTCAATTACAATAAAGCTCTTAAC
1826045 ATCATAGTACTATATCGTATTGTGATTGATAATATCACCATACTTTCTATTTTACTGTTTAGTTA
196 ATC--A-TACTATATCGTATTGTGATTGATAATATCACCATACTTTCTATTTTACTGTTTAGTTA
*
1826110 GT
258 GA
1826112 AATC
1 AATC
1826116 TTGTCAAATA
Statistics
Matches: 505, Mismatches: 15, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
258 64 0.13
259 376 0.74
260 4 0.01
261 61 0.12
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (259 bp):
AATCATTATGCTGCTCAAAATGAATGCAATTTTCCACCGCTCATAGGCTTTCCTAGTGCGGAACC
AATGGCATATGATTGATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTAC
TGTTGCACACCCATAACTGATAGAGATTGTAGTTTTCAAATTTCAATTACAATAAAGCTCTTAAC
ATCATACTATATCGTATTGTGATTGATAATATCACCATACTTTCTATTTTACTGTTTAGTTAGA
Found at i:1837473 original size:29 final size:30
Alignment explanation
Indices: 1837403--1837462 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1837393 CAATTTAAGG
1837403 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
*
1837434 CAAAATGTTTTTGGACTT-AATTGATTTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1837463 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.45
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1837587 original size:20 final size:21
Alignment explanation
Indices: 1837542--1837639 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 21
1837532 AGGGTGTCAA
1837542 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
1837563 AGTGCATCCATGCA-TCCTG-
1 AGTGCATCCATGCACCCCTGC
*
1837582 ATGTGCATCCATGCA--CATGCAC
1 A-GTGCATCCATGCACCCCTG--C
* *
1837604 TAGTGCATCGATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTGC
1837625 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1837640 TCAAACACCG
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
19 4 0.06
20 30 0.45
21 15 0.23
22 12 0.18
23 5 0.08
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1837685 original size:20 final size:20
Alignment explanation
Indices: 1837660--1837714 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1837650 AATGCAATTA
1837660 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
1837680 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
*
1837700 GTCCATCGATGCATC
1 GTGCATCGATGCATC
1837715 AAGGAGAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.16, C:0.31, G:0.20, T:0.33
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:1839228 original size:29 final size:31
Alignment explanation
Indices: 1839174--1839233 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1839164 AATTTAAGGC
*
1839174 AAAATGGTTTTTGGACTTGAATTGAATTTAT
1 AAAATGGTTTCTGGACTTGAATTGAATTTAT
1839205 AAAAT-GTTTCTGGACTT-AATTGAATTTAT
1 AAAATGGTTTCTGGACTTGAATTGAATTTAT
1839234 TCAAAGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 12 0.43
30 11 0.39
31 5 0.18
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (31 bp):
AAAATGGTTTCTGGACTTGAATTGAATTTAT
Found at i:1839354 original size:21 final size:21
Alignment explanation
Indices: 1839310--1839354 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1839300 AATGGGTGTC
*
1839310 GCAGTGCATCCATGCACCCCT
1 GCAGTGCATCCATGCACCCAT
*
1839331 GCAGTGCATCCATGCATCCAT
1 GCAGTGCATCCATGCACCCAT
1839352 GCA
1 GCA
1839355 CCTGCACTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
GCAGTGCATCCATGCACCCAT
Found at i:1840977 original size:84 final size:84
Alignment explanation
Indices: 1840836--1841005 Score: 315
Period size: 84 Copynumber: 2.0 Consensus size: 84
1840826 CTCGACGAGC
1840836 TAATTGGTTCCCTTCTCACTCATGAGATGATGGTGAAGGAAGATGAAGAAAGTGAAGAGAAGAAA
1 TAATTGGTTCCCTTCTCACTCATGAGATGATGGTGAAGGAAGATGAAGAAAGTGAAGAGAAGAAA
*
1840901 AATAATAAGAAGAAAGAGG
66 AACAATAAGAAGAAAGAGG
1840920 TAATTGGTTCCCTTCTCACTCATGAGATGATGGTGAAGGAAGATGAAGAAA-TGGAAGAGAAGAA
1 TAATTGGTTCCCTTCTCACTCATGAGATGATGGTGAAGGAAGATGAAGAAAGT-GAAGAGAAGAA
1840984 AAACAATAAGAAGAAAGAGG
65 AAACAATAAGAAGAAAGAGG
1841004 TA
1 TA
1841006 GACATTGCCT
Statistics
Matches: 84, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
83 1 0.01
84 83 0.99
ACGTcount: A:0.44, C:0.09, G:0.27, T:0.20
Consensus pattern (84 bp):
TAATTGGTTCCCTTCTCACTCATGAGATGATGGTGAAGGAAGATGAAGAAAGTGAAGAGAAGAAA
AACAATAAGAAGAAAGAGG
Found at i:1842851 original size:29 final size:31
Alignment explanation
Indices: 1842796--1842854 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1842786 AATTTAAGGT
*
1842796 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAATGGTTTCTGGACTTGAATTGAATTTAC
*
1842827 AAAAT-GTTTCTGGACTT-CATTGAATTTA
1 AAAATGGTTTCTGGACTTGAATTGAATTTA
1842855 TTCAAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 10 0.38
30 11 0.42
31 5 0.19
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.42
Consensus pattern (31 bp):
AAAATGGTTTCTGGACTTGAATTGAATTTAC
Found at i:1842960 original size:21 final size:21
Alignment explanation
Indices: 1842934--1843053 Score: 156
Period size: 21 Copynumber: 5.7 Consensus size: 21
1842924 AGGGTGTCAA
1842934 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
1842955 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
1842976 AGTGCATCCATGCATCCCTAC
1 AGTGCATCCATGCACCCCTGC
1842997 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCACCCCTG--C
* *
1843018 TAGTGCATCGATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTGC
1843039 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1843054 TCAAACACCA
Statistics
Matches: 88, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
19 3 0.03
20 13 0.15
21 56 0.64
22 13 0.15
23 3 0.03
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1843278 original size:20 final size:22
Alignment explanation
Indices: 1843240--1843279 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1843230 TTTGAGTAGA
1843240 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1843262 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1843280 ACATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1843845 original size:31 final size:30
Alignment explanation
Indices: 1843801--1843923 Score: 115
Period size: 30 Copynumber: 4.1 Consensus size: 30
1843791 AATCCCAACA
* *
1843801 AATTTCAATGGTCAAGTTAATATTTTATCT
1 AATTTCAAGGGTCAAATTAATATTTTATCT
* *
1843831 AAGTTTCAAGGGTCAAGTTGATA-TTTATCT
1 AA-TTTCAAGGGTCAAATTAATATTTTATCT
* * *
1843861 AATTTTTAAGGATCAAATTGATATTTTATCTT
1 AA-TTTCAAGGGTCAAATTAATATTTTATC-T
* * *
1843893 AATTTGAA-GGTCAAAATAATATTCTATCT
1 AATTTCAAGGGTCAAATTAATATTTTATCT
1843922 AA
1 AA
1843924 AATTTAGAGG
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
29 3 0.04
30 44 0.56
31 29 0.37
32 3 0.04
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (30 bp):
AATTTCAAGGGTCAAATTAATATTTTATCT
Found at i:1843860 original size:30 final size:31
Alignment explanation
Indices: 1843803--1843891 Score: 117
Period size: 30 Copynumber: 2.9 Consensus size: 31
1843793 TCCCAACAAA
* *
1843803 TTTCAATGGTCAAGTTAATATTTTATCTAAG
1 TTTCAAGGGTCAAGTTGATATTTTATCTAAG
*
1843834 TTTCAAGGGTCAAGTTGATA-TTTATCTAAT
1 TTTCAAGGGTCAAGTTGATATTTTATCTAAG
* * *
1843864 TTTTAAGGATCAAATTGATATTTTATCT
1 TTTCAAGGGTCAAGTTGATATTTTATCT
1843892 TAATTTGAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
30 26 0.51
31 25 0.49
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (31 bp):
TTTCAAGGGTCAAGTTGATATTTTATCTAAG
Found at i:1847025 original size:74 final size:72
Alignment explanation
Indices: 1846898--1847038 Score: 210
Period size: 74 Copynumber: 1.9 Consensus size: 72
1846888 AAAACCTTAA
* * * * **
1846898 GCAAGCAAAAGATACTATGCTTTGACCTAAACTTGTAACCCGATTGTTGAACAAGAATATGGAAT
1 GCAAACAAAAGATACCATACTTTGACCTAAAATTGTAACCCGATTGTCAAACAAG-A-ATGGAAT
1846963 TAGCCATAG
64 TAGCCATAG
1846972 GCAAACAAAAGATACCATACTTTGACCTAAAATTGTAACCCGATTGTCAAACAAGAATGGAATTA
1 GCAAACAAAAGATACCATACTTTGACCTAAAATTGTAACCCGATTGTCAAACAAGAATGGAATTA
1847037 GC
66 GC
1847039 AGGATATATA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 11 0.18
73 1 0.02
74 49 0.80
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.24
Consensus pattern (72 bp):
GCAAACAAAAGATACCATACTTTGACCTAAAATTGTAACCCGATTGTCAAACAAGAATGGAATTA
GCCATAG
Found at i:1873419 original size:12 final size:11
Alignment explanation
Indices: 1873402--1873427 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1873392 AAGTTTAAAT
1873402 AAAAAAAAAAC
1 AAAAAAAAAAC
1873413 AAAAAAAAAAC
1 AAAAAAAAAAC
1873424 AAAA
1 AAAA
1873428 GTCCGGACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:1883550 original size:20 final size:20
Alignment explanation
Indices: 1883517--1883555 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1883507 TCAACTAATA
* *
1883517 ATTTTTATCTAAATCAAACT
1 ATTTTTATCAAAATAAAACT
*
1883537 ATTTTTCTCAAAATAAAAC
1 ATTTTTATCAAAATAAAAC
1883556 GTTAAGAACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTTTATCAAAATAAAACT
Found at i:1887479 original size:18 final size:18
Alignment explanation
Indices: 1887458--1887495 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1887448 GATTTCACTT
*
1887458 ATTCCTCTCTTTTCT-TTA
1 ATTCC-CTCTATTCTCTTA
1887476 ATTCCCTCTATTCTCTTA
1 ATTCCCTCTATTCTCTTA
1887494 AT
1 AT
1887496 CTTATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTCCCTCTATTCTCTTA
Found at i:1889948 original size:32 final size:30
Alignment explanation
Indices: 1889907--1889976 Score: 104
Period size: 32 Copynumber: 2.3 Consensus size: 30
1889897 CCAGTTCAAT
*
1889907 AGAGTAAAGTATAATTAACCATAAAAGATGAG
1 AGAGAAAAGTATAATTAACCATAAAA-AT-AG
1889939 AGAGAAAAGTATAATTAACCATAAAAATAG
1 AGAGAAAAGTATAATTAACCATAAAAATAG
*
1889969 AGATAAAA
1 AGAGAAAA
1889977 ATCAAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 9 0.25
31 2 0.06
32 25 0.69
ACGTcount: A:0.59, C:0.06, G:0.16, T:0.20
Consensus pattern (30 bp):
AGAGAAAAGTATAATTAACCATAAAAATAG
Found at i:1890361 original size:16 final size:17
Alignment explanation
Indices: 1890340--1890373 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1890330 TTAGGTCGAA
*
1890340 TCAATTTTTGGGT-AGG
1 TCAATTTTCGGGTCAGG
1890356 TCAATTTTCGGGTCAGG
1 TCAATTTTCGGGTCAGG
1890373 T
1 T
1890374 GATTATCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.29, T:0.41
Consensus pattern (17 bp):
TCAATTTTCGGGTCAGG
Found at i:1892277 original size:16 final size:16
Alignment explanation
Indices: 1892256--1892334 Score: 88
Period size: 16 Copynumber: 5.0 Consensus size: 16
1892246 GTTTGGATTG
1892256 CTTTCGGTTCGGGTTA
1 CTTTCGGTTCGGGTTA
*
1892272 CTTTCGGATCGGGTTA
1 CTTTCGGTTCGGGTTA
** * * *
1892288 AATTCAGTTTGGGTTG
1 CTTTCGGTTCGGGTTA
1892304 CTTTCGGTTCGGGTTA
1 CTTTCGGTTCGGGTTA
*
1892320 -TTTTGGTTCGGGTTA
1 CTTTCGGTTCGGGTTA
1892335 AATTAGATAT
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
15 14 0.28
16 36 0.72
ACGTcount: A:0.10, C:0.14, G:0.32, T:0.44
Consensus pattern (16 bp):
CTTTCGGTTCGGGTTA
Found at i:1892309 original size:48 final size:47
Alignment explanation
Indices: 1892246--1892338 Score: 150
Period size: 48 Copynumber: 2.0 Consensus size: 47
1892236 AATTTTAGTT
1892246 GTTTGGATTGCTTTCGGTTCGGGTTACTTTCGGATCGGGTTAAATTCA
1 GTTTGGATTGCTTTCGGTTCGGGTTA-TTTCGGATCGGGTTAAATTCA
* * *
1892294 GTTTGGGTTGCTTTCGGTTCGGGTTATTTTGGTTCGGGTTAAATT
1 GTTTGGATTGCTTTCGGTTCGGGTTATTTCGGATCGGGTTAAATT
1892339 AGATATGGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 17 0.40
48 25 0.60
ACGTcount: A:0.12, C:0.12, G:0.31, T:0.45
Consensus pattern (47 bp):
GTTTGGATTGCTTTCGGTTCGGGTTATTTCGGATCGGGTTAAATTCA
Found at i:1893113 original size:11 final size:12
Alignment explanation
Indices: 1893082--1893114 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1893072 CATAATTACG
1893082 TATATAATATTT
1 TATATAATATTT
1893094 TAATATAATATTT
1 T-ATATAATATTT
1893107 T-TATAATA
1 TATATAATA
1893115 AGTTTGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.35
12 1 0.05
13 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATAATATTT
Found at i:1894746 original size:34 final size:34
Alignment explanation
Indices: 1894702--1894771 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
1894692 AACCATTTTT
* *
1894702 TTTCCGTTTCATATCGGATTTGGATGTACGCTTC
1 TTTCCATTTCATATCGGATTTGGATGTACACTTC
*
1894736 TTTCCATTTCATATTGGATTTGGATGTACACTTC
1 TTTCCATTTCATATCGGATTTGGATGTACACTTC
1894770 TT
1 TT
1894772 AATTTTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (34 bp):
TTTCCATTTCATATCGGATTTGGATGTACACTTC
Found at i:1895920 original size:12 final size:12
Alignment explanation
Indices: 1895903--1895928 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1895893 CTATGGTGAC
1895903 TCTTATAATTTA
1 TCTTATAATTTA
1895915 TCTTATAATTTA
1 TCTTATAATTTA
1895927 TC
1 TC
1895929 GGACAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.58
Consensus pattern (12 bp):
TCTTATAATTTA
Found at i:1907674 original size:11 final size:11
Alignment explanation
Indices: 1907658--1907686 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1907648 GCAACAAACA
1907658 CAGCAACAATT
1 CAGCAACAATT
1907669 CAGCAACAATT
1 CAGCAACAATT
1907680 CAGCAAC
1 CAGCAAC
1907687 CTCCTATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.31, G:0.10, T:0.14
Consensus pattern (11 bp):
CAGCAACAATT
Found at i:1913581 original size:370 final size:375
Alignment explanation
Indices: 1912893--1913629 Score: 1369
Period size: 370 Copynumber: 2.0 Consensus size: 375
1912883 GAATAACTCG
1912893 AAAAAATATATATATATGAAACAAGGGACAGCCATGTATGAAAAAATATGAAGAAATATATATGT
1 AAAAAATATATATATATGAAACAAGGGACAGCCATGTATGAAAAAATATGAAGAAATATATATGT
*
1912958 ATTGTATATGATTATAAAAAATCATTTAAATTAGAATCAAATACTATCATAATATTGTAAATACT
66 ATTG-ATATGATTATAAAAAATCATTTAAATTAGAATCAAATACTATCATAATATTATAAATACT
1913023 TACAATTCAATTTAAACAGAAACTCGAAAACTCGACTCGAATGTATTAACTTGACTCAACTCAAA
130 TACAATTCAATTTAAACAGAAACTCGAAAACTCGACTCGAATGTATTAACTTGACTCAACTCAAA
1913088 AATTTTCTAATTAAGTTTGAGTTATAAAATAGAAATTGTCAACTCGAATAACTCAAAAAAAATTA
195 AATTTTCTAATTAAGTTTGAGTTATAAAATAGAAATTGTCAACTCGAATAACTCAAAAAAAATTA
*
1913153 CTCTACTCGATCAAATGCTCACTCCTACCTCTAAAGACAATACGTAGAATTTTATGTTAGGGAAT
260 CTCTACTCGATCAAATGCTCACTCCTACCTCTAAAGACAATACATAGAATTTTATGTTAGGGAAT
*
1913218 GACTTTATAAAATTTTAAGAAAACAAATATATATATATTAATATAAGTATGA
325 GACTTTATAAAATTTTAAGAAAACAAATATAGA-ATATTAATATAAGTATGA
*
1913270 AAAAAATATATATATATGAAACAAGGGACATCCATGTATGAAAAAATATGAAG-AA-ATATATGT
1 AAAAAATATATATATATGAAACAAGGGACAGCCATGTATGAAAAAATATGAAGAAATATATATGT
1913333 A-TG-TATGATTATAAAAAATCATTTAAA-TAGAATCAAATACTATCATAATATTAT-AATACTT
66 ATTGATATGATTATAAAAAATCATTTAAATTAGAATCAAATACTATCATAATATTATAAATACTT
*
1913394 ACAATTCAATTTAAACAGAAACTCGAAAACTCGACTCGAATGTATTAACTTGACTCTACTCAAAA
131 ACAATTCAATTTAAACAGAAACTCGAAAACTCGACTCGAATGTATTAACTTGACTCAACTCAAAA
1913459 ATTTTCTAATTAAGTTTGAGTTATAAAATAGAAATTGTCAACTCGAATAACTCAAAAAAAATTAC
196 ATTTTCTAATTAAGTTTGAGTTATAAAATAGAAATTGTCAACTCGAATAACTCAAAAAAAATTAC
1913524 TCTACTCGATCAAATGCTCACTCCTACCTCTAAAGACAATACATAGAATTTTATGTTAGGGAATG
261 TCTACTCGATCAAATGCTCACTCCTACCTCTAAAGACAATACATAGAATTTTATGTTAGGGAATG
1913589 ACTTTATAAAATTTTAAGAAAACAAATATAGAATATTAATA
326 ACTTTATAAAATTTTAAGAAAACAAATATAGAATATTAATA
1913630 GAAAATACAA
Statistics
Matches: 355, Mismatches: 5, Indels: 8
0.96 0.01 0.02
Matches are distributed among these distances:
369 9 0.03
370 231 0.65
371 26 0.07
372 24 0.07
374 2 0.01
375 9 0.03
376 2 0.01
377 52 0.15
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (375 bp):
AAAAAATATATATATATGAAACAAGGGACAGCCATGTATGAAAAAATATGAAGAAATATATATGT
ATTGATATGATTATAAAAAATCATTTAAATTAGAATCAAATACTATCATAATATTATAAATACTT
ACAATTCAATTTAAACAGAAACTCGAAAACTCGACTCGAATGTATTAACTTGACTCAACTCAAAA
ATTTTCTAATTAAGTTTGAGTTATAAAATAGAAATTGTCAACTCGAATAACTCAAAAAAAATTAC
TCTACTCGATCAAATGCTCACTCCTACCTCTAAAGACAATACATAGAATTTTATGTTAGGGAATG
ACTTTATAAAATTTTAAGAAAACAAATATAGAATATTAATATAAGTATGA
Found at i:1913899 original size:3 final size:3
Alignment explanation
Indices: 1913891--1913924 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1913881 TAAAATCCAA
1913891 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1913925 GAGAGTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1914449 original size:37 final size:37
Alignment explanation
Indices: 1914400--1914504 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1914390 GTGCTTGTGG
* *
1914400 ATCATATATTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * * *
1914437 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* *
1914474 ATCATATTTTTATGAGTTTGAATCCTAGTAG
1 ATCATATTTTTAGGAGTTTGAATCATAGTAG
1914505 GACGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:1915526 original size:106 final size:106
Alignment explanation
Indices: 1915234--1916698 Score: 1916
Period size: 106 Copynumber: 14.0 Consensus size: 106
1915224 GCATTGTTCC
* * ** * **
1915234 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGGTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * * *
1915298 ACCAATC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACC-AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
1915340 GAGTCTGATATCCTTCGCTGTGAAGTTGAAATTGACTCT-AAA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * ** *
1915399 TCAGCCG-CCCTTTCGTCGTGAAGTTGAGTTTACGTTGTCATG
66 CCAGCGGTCCC-TTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
1915441 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * **
1915505 TCAGCCG-CCCTTTCGTCGTGAAGTTGAGTTTGCGTTGTCTTG
66 CCAGCGGTCCC-TTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
1915547 G-GTCCAAGATCCTTCGTTGAGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1915611 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1915652 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1915717 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1915758 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1915823 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1915864 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTAGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1915929 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
1915970 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1916035 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1916076 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1916140 CCAGCGGTCCCTTCGTTGTGAA----AACTTGC---GTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1916174 GAGTCCAATATCCTTCGCTGTGAAGTT-AAGATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAA-ATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
*
1916238 ACCAAG-GGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
65 ACC-AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1916280 GAGTCCAATATCCTTCGTTGTGAAGTTGAAA-TGGCTCTGAAATTGAG-A-TTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1916342 -CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1916382 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAA--AGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1916444 CCAGCGGTCCCTTCGTCGTG-AGTTGAACTTGTGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1916484 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1916549 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** * * *
1916590 GAGTCCAATATCCTTCGCTGTGAAGTTGAAAATTGGCTCCGAAATT-GGAAAAT-TATGTTGTCA
1 GAGTCCAATATCCTTCGCTGTGAAGTTG-AAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
** * * *
1916653 A-CAGCCATCCCTTCGTTGTGAAGTTTGAACTTGTGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAG-TTGAACTTGCGTTGTCTG
1916695 GAGT
1 GAGT
1916699 GGCACGATAT
Statistics
Matches: 1227, Mismatches: 99, Indels: 67
0.88 0.07 0.05
Matches are distributed among these distances:
97 2 0.00
98 48 0.04
99 38 0.03
100 68 0.06
101 15 0.01
102 144 0.12
103 56 0.05
104 23 0.02
105 116 0.09
106 695 0.57
107 22 0.02
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1917541 original size:22 final size:22
Alignment explanation
Indices: 1917515--1917557 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1917505 TTGTGTTTGG
*
1917515 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTAGCATTTGATGC
*
1917537 TCAAAGGTTTAGTATTTGATG
1 TCAAAGGTTTAGCATTTGATG
1917558 TGGTAGCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (22 bp):
TCAAAGGTTTAGCATTTGATGC
Found at i:1921475 original size:19 final size:20
Alignment explanation
Indices: 1921447--1921484 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1921437 TGCATATGAT
*
1921447 GGAAATAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
1921466 GGAAAAAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
1921485 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:1922636 original size:37 final size:37
Alignment explanation
Indices: 1922595--1922690 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 37
1922585 GGATCCTATC
* *
1922595 TTTAGGAGTTTAAATCATAGTAAAACTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGTAAAACTCTATCATATT
* * *
1922632 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAAAACTCTATCATATT
*
1922669 TTTATGAGTTTGAATCCTAGTA
1 TTTAGGAGTTTGAATCCTAGTA
1922691 GGACGAAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAAAACTCTATCATATT
Found at i:1927333 original size:25 final size:26
Alignment explanation
Indices: 1927305--1927353 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
1927295 TTTTACTCCT
* *
1927305 AATTAATTCGATAGAC-AATTCAATA
1 AATTAAATCCATAGACAAATTCAATA
*
1927330 AATTAAATCCATATACAAATTCAA
1 AATTAAATCCATAGACAAATTCAA
1927354 ATAATAATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (26 bp):
AATTAAATCCATAGACAAATTCAATA
Found at i:1931972 original size:80 final size:81
Alignment explanation
Indices: 1931876--1932038 Score: 265
Period size: 80 Copynumber: 2.0 Consensus size: 81
1931866 AGTTGCCGTC
* * *
1931876 GCACCTTGTGAAGCCATGGCCTTCATTGATTGGCTATGTTGATCCA-TCCATCGAGCATCAATAA
1 GCACCTTGTGAAGCCATGACCTTCATTGATTGGCCACGTTGATCCATTCCATCGAGCATCAATAA
* **
1931940 TCCGCCTTCGAGATTT
66 TCCACCGCCGAGATTT
1931956 GCACCTTGTGAAGCCATGACCTTCATTGATTGGCCACGTTGATCCATTCCATCGAGCATCAATAA
1 GCACCTTGTGAAGCCATGACCTTCATTGATTGGCCACGTTGATCCATTCCATCGAGCATCAATAA
1932021 TCCACCGCCGAGATTT
66 TCCACCGCCGAGATTT
1932037 GC
1 GC
1932039 TTTCTGATGG
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
80 43 0.57
81 33 0.43
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (81 bp):
GCACCTTGTGAAGCCATGACCTTCATTGATTGGCCACGTTGATCCATTCCATCGAGCATCAATAA
TCCACCGCCGAGATTT
Found at i:1938277 original size:26 final size:26
Alignment explanation
Indices: 1938241--1938303 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
1938231 CCTCCACTCG
*
1938241 ACCCGACCCGAATATATGAATTAGAA
1 ACCCGACCCGAATATATAAATTAGAA
1938267 ACCCGACCCGAATATATAAATTAGAA
1 ACCCGACCCGAATATATAAATTAGAA
* *
1938293 ACTCGAACCGA
1 ACCCGACCCGA
1938304 CCAGAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.17
Consensus pattern (26 bp):
ACCCGACCCGAATATATAAATTAGAA
Found at i:1938502 original size:27 final size:27
Alignment explanation
Indices: 1938472--1938537 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
1938462 CCTAAACCCG
1938472 AACCCGACCCGAA-ATCACACTTTAAAA
1 AACCCGACCCGAATATCACAC-TTAAAA
1938499 AACCCGACCCGAATATCACACTTAAAA
1 AACCCGACCCGAATATCACACTTAAAA
* *
1938526 AACTCGATCCGA
1 AACCCGACCCGA
1938538 CCTGATTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 29 0.81
28 7 0.19
ACGTcount: A:0.42, C:0.33, G:0.09, T:0.15
Consensus pattern (27 bp):
AACCCGACCCGAATATCACACTTAAAA
Found at i:1938526 original size:28 final size:27
Alignment explanation
Indices: 1938472--1938527 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 27
1938462 CCTAAACCCG
*
1938472 AACCCGACCCGAAATCACACTTTAAAA
1 AACCCGACCCGAAATCACACTTAAAAA
1938499 AACCCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGAA-ATCACACTTAAAAA
1938527 A
1 A
1938528 CTCGATCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.46, C:0.32, G:0.07, T:0.14
Consensus pattern (27 bp):
AACCCGACCCGAAATCACACTTAAAAA
Found at i:1940416 original size:11 final size:11
Alignment explanation
Indices: 1940402--1940428 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1940392 AATATTAAAT
1940402 ATAAAAAATAA
1 ATAAAAAATAA
1940413 ATAAAAAATAA
1 ATAAAAAATAA
1940424 ATAAA
1 ATAAA
1940429 TGAATGTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:1940809 original size:12 final size:13
Alignment explanation
Indices: 1940792--1940821 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1940782 TATTTTTAAA
1940792 TAAAATAT-TATT
1 TAAAATATATATT
1940804 TAAAATATATATT
1 TAAAATATATATT
1940817 TAAAA
1 TAAAA
1940822 AAAATCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAAAATATATATT
Found at i:1943935 original size:167 final size:167
Alignment explanation
Indices: 1943759--1944063 Score: 601
Period size: 167 Copynumber: 1.8 Consensus size: 167
1943749 TTTTATGATT
*
1943759 TTTTTAATTTTAATTTTATAATAAATAATACGTTCTATTTTGATTAAATATATTTTAACAAAAAT
1 TTTTTAATTTTAATTTTATAATAAATAATACGTTCTAATTTGATTAAATATATTTTAACAAAAAT
1943824 GTATCAAATAATATATAAATAAATAAATATACAGTGGAAAAATGAAAAATATAGTAAACTACAAA
66 GTATCAAATAATATATAAATAAATAAATATACAGTGGAAAAATGAAAAATATAGTAAACTACAAA
1943889 GATGATGAAAAATATTTATATTTTTTATTTGTTTTAC
131 GATGATGAAAAATATTTATATTTTTTATTTGTTTTAC
1943926 TTTTTAATTTTAATTTTATAATAAATAATACGTTCTAATTTGATTAAATATATTTTAACAAAAAT
1 TTTTTAATTTTAATTTTATAATAAATAATACGTTCTAATTTGATTAAATATATTTTAACAAAAAT
1943991 GTATCAAATAATATATAAATAAATAAATATACAGTGGAAAAATGAAAAATATAGTAAACTACAAA
66 GTATCAAATAATATATAAATAAATAAATATACAGTGGAAAAATGAAAAATATAGTAAACTACAAA
1944056 GATGATGA
131 GATGATGA
1944064 CATATTAAGC
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 137 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.39
Consensus pattern (167 bp):
TTTTTAATTTTAATTTTATAATAAATAATACGTTCTAATTTGATTAAATATATTTTAACAAAAAT
GTATCAAATAATATATAAATAAATAAATATACAGTGGAAAAATGAAAAATATAGTAAACTACAAA
GATGATGAAAAATATTTATATTTTTTATTTGTTTTAC
Found at i:1945976 original size:20 final size:19
Alignment explanation
Indices: 1945923--1945978 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1945913 ATACTGAGTT
1945923 GGTAT-TATCGATACCATG
1 GGTATGTATCGATACCATG
*
1945941 GGTATTTATCGATACCATG
1 GGTATGTATCGATACCATG
* *
1945960 TGTATAGTATTGATACCAT
1 GGTAT-GTATCGATACCAT
1945979 TTTCAAGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 5 0.15
19 17 0.52
20 11 0.33
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.38
Consensus pattern (19 bp):
GGTATGTATCGATACCATG
Found at i:1948142 original size:18 final size:18
Alignment explanation
Indices: 1948111--1948181 Score: 115
Period size: 18 Copynumber: 3.9 Consensus size: 18
1948101 GCATAGAATT
*
1948111 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1948129 TGTTCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
1948147 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1948165 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1948182 GATAATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1951327 original size:35 final size:34
Alignment explanation
Indices: 1951286--1951386 Score: 168
Period size: 35 Copynumber: 2.9 Consensus size: 34
1951276 CTAAACCCTA
*
1951286 AATTAAAGTATTTTAGAATTTAGGGTTTAAAATGT
1 AATTAAATTATTTTAGAATTT-GGGTTTAAAATGT
1951321 AATTAAATTATTTTAGAATTTGGGGTTTAAAATGT
1 AATTAAATTATTTTAGAATTT-GGGTTTAAAATGT
1951356 AATTAAATTATTTTA-AATTTGGGTTTAAAAT
1 AATTAAATTATTTTAGAATTTGGGTTTAAAAT
1951387 AAAATTGAGG
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
33 11 0.17
34 5 0.08
35 48 0.75
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (34 bp):
AATTAAATTATTTTAGAATTTGGGTTTAAAATGT
Done.