Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007845.1 Hibiscus syriacus cultivar Beakdansim tig00110201_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: 2731752
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 9 of 13
Found at i:1799209 original size:22 final size:22
Alignment explanation
Indices: 1799181--1799308 Score: 204
Period size: 22 Copynumber: 5.8 Consensus size: 22
1799171 ACTTTTAACA
1799181 CCATATTTTAAAATAAATCAAT
1 CCATATTTTAAAATAAATCAAT
*
1799203 CCATATTTTAAAATAATTCAAT
1 CCATATTTTAAAATAAATCAAT
**
1799225 CCATATTTTAAAATAAAAT-TTT
1 CCATATTTTAAAAT-AAATCAAT
1799247 CCATATTTTAAAATAAATCAAT
1 CCATATTTTAAAATAAATCAAT
1799269 CCATATTTTAAAATAAATCAAT
1 CCATATTTTAAAATAAATCAAT
*
1799291 CAATATTTTAAAATAAAT
1 CCATATTTTAAAATAAAT
1799309 TTTAAAATAG
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
21 4 0.04
22 90 0.93
23 3 0.03
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (22 bp):
CCATATTTTAAAATAAATCAAT
Found at i:1805090 original size:23 final size:25
Alignment explanation
Indices: 1805042--1805091 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
1805032 AATTCCTAAA
1805042 GAAGAAAACAAATGGGAGAGGGAGAAC
1 GAAGAAAACAAATGGGAGA--GAGAAC
1805069 GAAGAAAACAAATGGG-GA-AGAAC
1 GAAGAAAACAAATGGGAGAGAGAAC
1805092 TTTTTGGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.22
26 2 0.09
27 16 0.70
ACGTcount: A:0.54, C:0.08, G:0.34, T:0.04
Consensus pattern (25 bp):
GAAGAAAACAAATGGGAGAGAGAAC
Found at i:1806919 original size:21 final size:21
Alignment explanation
Indices: 1806890--1806941 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1806880 TTGTAGCGAT
*
1806890 CATCATTCTTGTTATGAGGTC
1 CATCTTTCTTGTTATGAGGTC
1806911 CATCTTTCTTGTTATGAGGTC
1 CATCTTTCTTGTTATGAGGTC
*
1806932 CATATTTCTT
1 CATCTTTCTT
1806942 TGTAAATACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.48
Consensus pattern (21 bp):
CATCTTTCTTGTTATGAGGTC
Found at i:1814596 original size:23 final size:23
Alignment explanation
Indices: 1814570--1814617 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1814560 AAAAAGTACA
*
1814570 ATAACATACTAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
* *
1814593 ATAATATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
1814616 AT
1 AT
1814618 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:1815139 original size:22 final size:22
Alignment explanation
Indices: 1815084--1815160 Score: 111
Period size: 23 Copynumber: 3.5 Consensus size: 22
1815074 TGATAGATAT
*
1815084 TTACA-ATATAAGCACTACCTA
1 TTACATATATAAGCGCTACCTA
*
1815105 TTACATTATATAAACGCTACCTA
1 TTACA-TATATAAGCGCTACCTA
1815128 TTACATATATAAGCGCTACCTA
1 TTACATATATAAGCGCTACCTA
1815150 TTACATCATAT
1 TTACAT-ATAT
1815161 TTTTACTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
21 5 0.10
22 22 0.44
23 23 0.46
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACATATATAAGCGCTACCTA
Found at i:1815312 original size:26 final size:28
Alignment explanation
Indices: 1815283--1815339 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
1815273 CTACAATATT
1815283 AATTTA-ATAATT-TCATTTGCACAAAA
1 AATTTATATAATTGTCATTTGCACAAAA
* *
1815309 AA-TTATTTGATTGTCATTTGCACAAAA
1 AATTTATATAATTGTCATTTGCACAAAA
1815336 AATT
1 AATT
1815340 ATTTGATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 3 0.12
26 6 0.23
27 16 0.62
28 1 0.04
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (28 bp):
AATTTATATAATTGTCATTTGCACAAAA
Found at i:1815325 original size:27 final size:27
Alignment explanation
Indices: 1815295--1815349 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1815285 TTTAATAATT
1815295 TCATTTGCACAAAAAATTATTTGATTG
1 TCATTTGCACAAAAAATTATTTGATTG
1815322 TCATTTGCACAAAAAATTATTTGATTG
1 TCATTTGCACAAAAAATTATTTGATTG
1815349 T
1 T
1815350 TTTGATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (27 bp):
TCATTTGCACAAAAAATTATTTGATTG
Found at i:1815635 original size:23 final size:23
Alignment explanation
Indices: 1815600--1815672 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1815590 ATACTTTACA
*
1815600 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
1815623 ATATAAACGCTACATATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1815646 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
1815669 ATAT
1 ATAT
1815673 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:1816144 original size:23 final size:23
Alignment explanation
Indices: 1816095--1816156 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1816085 ATATAAGTAT
1816095 TACCTATTACATTAT-TAAACGC
1 TACCTATTACATTATATAAACGC
*
1816117 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGC
*
1816140 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1816157 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 15 0.41
23 22 0.59
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGC
Found at i:1816250 original size:484 final size:485
Alignment explanation
Indices: 1815322--1816401 Score: 1891
Period size: 484 Copynumber: 2.2 Consensus size: 485
1815312 TATTTGATTG
* * *
1815322 TCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATT
1 TCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATT
*
1815387 TAACAAAATTAACCAAAGATAATAAT-AATATGTAATATATATGTTTATTGTTTTTAATTTAATA
66 TAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATA
1815451 ATAATATATCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
131 ATAATATATCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
1815516 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAA
196 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAA
*
1815581 AAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACATATTACATT
261 AAAAGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACATATTACATT
1815646 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATA
326 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATA
* *
1815711 AAAAATATCGATAATTTTTTAAAGTTATGTAATTAATGTTTCAATTTTTTTAATAGTGTTTCATA
391 AAAAAGACCGATAATTTTTTAAAGTTATGTAATTAATGTTTCAATTTTTTTAATAGTGTTTCATA
1815776 TTTTCCACCTACAATATTAATTTAATAATT
456 TTTTCCACCTACAATATTAATTTAATAATT
1815806 TCATTTACACAAAAAATTA-TTGATTGTTTTGATATTTTATAAAATATTATTTA-TA-TTAAATT
1 TCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATT
* * * *
1815868 TAACAATATTAACAAAAGATAATAATAAAAATATAATATACATGTTTATTGTTTTTAATTTAATA
66 TAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATA
** *
1815933 ATAATATATACCGTATTGTAAAAAATAAATCATTATACGCCTATAATTACTAAATTAATATCTTA
131 ATAATATAT--CGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTA
*
1815998 AAACTCACTCAAAATATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTA
193 AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTA
* * * *
1816063 TAAAAAATATAGATACTTTACAATATAAGTATTACCTATTACATTAT-TAAACGCTACCTATTAC
258 TAAAAAAGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACATATTAC
1816127 ATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTT
323 ATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTT
* *
1816192 ATAAAAAGGACCGATACTTTTTTAAAGTTATGTAATTAATGTTTCAATTTTTTTAATAGTGTTTC
388 ATAAAAAAGACCGATAATTTTTTAAAGTTATGTAATTAATGTTTCAATTTTTTTAATAGTGTTTC
* *
1816257 ATGTTTTTCACCTACAATATTAATTTAATAATT
453 ATATTTTCCACCTACAATATTAATTTAATAATT
1816290 TCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATT
1 TCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATT
1816355 TAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTTT
66 TAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTTT
1816402 GCCATTCATT
Statistics
Matches: 562, Mismatches: 27, Indels: 11
0.94 0.05 0.02
Matches are distributed among these distances:
481 31 0.06
482 45 0.08
483 33 0.06
484 216 0.38
485 185 0.33
486 2 0.00
487 50 0.09
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (485 bp):
TCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATT
TAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATA
ATAATATATCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAA
AAAAGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACATATTACATT
ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATA
AAAAAGACCGATAATTTTTTAAAGTTATGTAATTAATGTTTCAATTTTTTTAATAGTGTTTCATA
TTTTCCACCTACAATATTAATTTAATAATT
Found at i:1816740 original size:200 final size:200
Alignment explanation
Indices: 1816397--1817002 Score: 1068
Period size: 200 Copynumber: 3.0 Consensus size: 200
1816387 GTAATATATA
* *
1816397 TGTTTGCCATTCATTCTGGACTAGAAATATCAACACAAACTACAAAAGTGTCGATACATTATTTA
1 TGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
*
1816462 GACTTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTA
66 GACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTA
* *
1816527 TTCTTTTGGTTTTCGATGTTTATGGGATCGATAATTTTTATATATGGATCGACACTTTATGGTTG
131 TTCTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTG
1816592 CACCC
196 CACCC
*
1816597 TGTTTGCCATTCATTCTGGACCAGAAATATCGTCACAAACTACAAAAGTGTCGATACATTATTTA
1 TGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
*
1816662 GACCTATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTA
66 GACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTA
*
1816727 TTCTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATAGATCGACACTTTATGGTTG
131 TTCTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTG
1816792 CACCC
196 CACCC
1816797 TGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
1 TGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
* * *
1816862 GACCTATTCTCTCATAAAACCGGTATACTTGCACCGATTAGATTGAAAAATTACCTATTACATTA
66 GACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTA
* * * *
1816927 TACTTTTGGGTTTCGATATTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTG
131 TTCTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTG
*
1816992 CACCT
196 CACCC
1816997 TGTTTG
1 TGTTTG
1817003 TCATATTGTA
Statistics
Matches: 387, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
200 387 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (200 bp):
TGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
GACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTA
TTCTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTG
CACCC
Found at i:1817129 original size:18 final size:18
Alignment explanation
Indices: 1817106--1817166 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1817096 TCTCATTCAT
*
1817106 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
1817124 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
1817143 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
1817162 AATTA
1 AATTA
1817167 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:1817142 original size:19 final size:19
Alignment explanation
Indices: 1817118--1817166 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1817108 TTATATTCAC
1817118 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1817137 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1817156 ATACAAAATTA
1 ATACAAAATTA
1817167 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1818969 original size:21 final size:21
Alignment explanation
Indices: 1818943--1818995 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1818933 TCTCAAGGTA
*
1818943 TCTTCGACTCTCTCAAGTTTC
1 TCTTCGACTCTATCAAGTTTC
1818964 TCTTCGACTCTATCAAGTTTC
1 TCTTCGACTCTATCAAGTTTC
1818985 TCTTCGACTCT
1 TCTTCGACTCT
1818996 TGATGTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.32, G:0.09, T:0.43
Consensus pattern (21 bp):
TCTTCGACTCTATCAAGTTTC
Found at i:1821414 original size:20 final size:20
Alignment explanation
Indices: 1821387--1821433 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1821377 TCCGGTAACG
1821387 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
1821406 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
1821427 TTTTACC
1 TTTTACC
1821434 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:1821661 original size:182 final size:181
Alignment explanation
Indices: 1821173--1821646 Score: 723
Period size: 181 Copynumber: 2.6 Consensus size: 181
1821163 CGTACTTACG
* * *
1821173 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACAGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1821238 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTTAAAGTATCGACACATTAT
*
1821303 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
*
1821354 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1821419 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTTAAAAGTATCGACACTTTA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTT-AAAGTATCGACACATTA
** *
1821484 TAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 TAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * * **
1821537 AAAGTACCGATACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1821602 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1821647 AATTTAGATC
Statistics
Matches: 266, Mismatches: 25, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
181 105 0.39
182 63 0.24
183 98 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTTAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:1825694 original size:16 final size:17
Alignment explanation
Indices: 1825659--1825695 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1825649 TATGGATGAA
1825659 AAAAATAGTATTATTAT
1 AAAAATAGTATTATTAT
1825676 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTAT
1825692 AAAA
1 AAAA
1825696 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTAT
Found at i:1827239 original size:2 final size:2
Alignment explanation
Indices: 1827232--1827263 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1827222 AACGTTTGCA
1827232 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
1827264 TATCAGTGAT
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:1827931 original size:20 final size:20
Alignment explanation
Indices: 1827906--1827943 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1827896 TCATCAAAGT
* *
1827906 GAAGAATATGAATTAAATAC
1 GAAGAATACGAATCAAATAC
1827926 GAAGAATACGAATCAAAT
1 GAAGAATACGAATCAAAT
1827944 GTAGAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.08, G:0.16, T:0.21
Consensus pattern (20 bp):
GAAGAATACGAATCAAATAC
Found at i:1828348 original size:3 final size:3
Alignment explanation
Indices: 1828333--1828373 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
1828323 TTAAAATTCA
* *
1828333 TAT TAT TAC TAT TAT TATT TAA TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
1828374 TTAAAGGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1828360 original size:22 final size:22
Alignment explanation
Indices: 1828332--1828374 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1828322 TTTAAAATTC
1828332 ATATTATTACTATTATTATTTA
1 ATATTATTACTATTATTATTTA
*
1828354 ATATTATTATTATTATTATTT
1 ATATTATTACTATTATTATTT
1828375 TAAAGGCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATTATTACTATTATTATTTA
Found at i:1828448 original size:40 final size:39
Alignment explanation
Indices: 1828404--1828500 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 39
1828394 TTGAACGTAA
* *
1828404 TATAATTATATTTATTTGATTTA-AAGTAAGAAGTTT-GATT
1 TATAATTATATTTATTTAATTTATAAGT--GAA-TTTCAATT
*
1828444 TATAATTATATTTAATTAATTTATAAGTGAATTTCAATT
1 TATAATTATATTTATTTAATTTATAAGTGAATTTCAATT
*
1828483 TATAATTATTTTTTATTT
1 TATAATTA-TATTTATTT
1828501 TTTATATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
38 3 0.06
39 14 0.29
40 28 0.57
41 4 0.08
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.55
Consensus pattern (39 bp):
TATAATTATATTTATTTAATTTATAAGTGAATTTCAATT
Found at i:1831999 original size:37 final size:37
Alignment explanation
Indices: 1831958--1832032 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
1831948 ATTATATTGG
1831958 TCAATAAATTCCACGGAATATAATGATTATGTTTTCT
1 TCAATAAATTCCACGGAATATAATGATTATGTTTTCT
1831995 TCAATAAATTCCACGGAATATAATGATTATGTTTTCT
1 TCAATAAATTCCACGGAATATAATGATTATGTTTTCT
1832032 T
1 T
1832033 AGTTTCGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (37 bp):
TCAATAAATTCCACGGAATATAATGATTATGTTTTCT
Found at i:1835590 original size:2 final size:2
Alignment explanation
Indices: 1835583--1835607 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1835573 AATAAATTCA
1835583 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
1835608 ACCACTAGTT
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:1840935 original size:42 final size:42
Alignment explanation
Indices: 1840876--1840959 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
1840866 GGACCACAAG
1840876 CCCAATCTAATGCAGTCTGTAAGTTCGTTTGAGAAGCCTGCC
1 CCCAATCTAATGCAGTCTGTAAGTTCGTTTGAGAAGCCTGCC
1840918 CCCAATCTAATGCAGTCTGTAAGTTCGTTTGAGAAGCCTGCC
1 CCCAATCTAATGCAGTCTGTAAGTTCGTTTGAGAAGCCTGCC
1840960 TAGAAGCAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (42 bp):
CCCAATCTAATGCAGTCTGTAAGTTCGTTTGAGAAGCCTGCC
Found at i:1843059 original size:36 final size:36
Alignment explanation
Indices: 1843019--1843090 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1843009 CATGTTGATA
1843019 ATGCTCAAATTAGGTTA-ACCCACTAGTATTGGAAAT
1 ATGCTCAAATTAGGTTATA-CCACTAGTATTGGAAAT
1843055 ATGCTCAAATTAGGTTATACCACTAGTATTGGAAAT
1 ATGCTCAAATTAGGTTATACCACTAGTATTGGAAAT
1843091 GACACCAGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 34 0.97
37 1 0.03
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (36 bp):
ATGCTCAAATTAGGTTATACCACTAGTATTGGAAAT
Found at i:1845132 original size:36 final size:36
Alignment explanation
Indices: 1845085--1845165 Score: 155
Period size: 36 Copynumber: 2.3 Consensus size: 36
1845075 GTCTAGCCAT
1845085 GTATTAGAAATATGCTCAAATTAGGTTATACCACTA
1 GTATTAGAAATATGCTCAAATTAGGTTATACCACTA
1845121 GTATTAGAAATATGCTCAAATTAGGTTATACCACTA
1 GTATTAGAAATATGCTCAAATTAGGTTATACCACTA
1845157 GTATT-GAAA
1 GTATTAGAAA
1845166 ATGATGATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 4 0.09
36 41 0.91
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (36 bp):
GTATTAGAAATATGCTCAAATTAGGTTATACCACTA
Found at i:1846104 original size:5 final size:5
Alignment explanation
Indices: 1846091--1846122 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1846081 AATATTATTT
*
1846091 TTATG TTATA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TT
1846123 TTATATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:1848350 original size:20 final size:20
Alignment explanation
Indices: 1848325--1848362 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1848315 TCATCAAAAT
* *
1848325 GAAGAATATGAATTAAATAC
1 GAAGAATACGAATCAAATAC
1848345 GAAGAATACGAATCAAAT
1 GAAGAATACGAATCAAAT
1848363 GTAGAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.08, G:0.16, T:0.21
Consensus pattern (20 bp):
GAAGAATACGAATCAAATAC
Found at i:1848851 original size:40 final size:39
Alignment explanation
Indices: 1848807--1848894 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 39
1848797 TTGAACGTAA
* * *
1848807 TATAATTATATTTATTTGATTTA-AAGTAAGAAGTTT-GATT
1 TATAATTATATTTAATTAATTTATAAGT--GAA-TTTCAATT
1848847 TATAATTATATTTAATTAATTTATAAGTGAATTTCAATT
1 TATAATTATATTTAATTAATTTATAAGTGAATTTCAATT
1848886 TATAATTAT
1 TATAATTAT
1848895 TTTTTTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 3 0.07
39 15 0.35
40 21 0.49
41 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.08, T:0.51
Consensus pattern (39 bp):
TATAATTATATTTAATTAATTTATAAGTGAATTTCAATT
Found at i:1849099 original size:15 final size:15
Alignment explanation
Indices: 1849079--1849110 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1849069 TAATTTATAT
1849079 ATAATACAAATATTA
1 ATAATACAAATATTA
*
1849094 ATAATATAAATATTA
1 ATAATACAAATATTA
1849109 AT
1 AT
1849111 TTATATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATACAAATATTA
Found at i:1850176 original size:111 final size:111
Alignment explanation
Indices: 1849982--1850205 Score: 448
Period size: 111 Copynumber: 2.0 Consensus size: 111
1849972 ATATAGTTTA
1849982 CCCGTCTTCCCACGCAACGTTGTAGCTCATCTCTTCAAACTCCTAATCCTGCTGAATGTCTCAAT
1 CCCGTCTTCCCACGCAACGTTGTAGCTCATCTCTTCAAACTCCTAATCCTGCTGAATGTCTCAAT
1850047 CTTTATAACACCAAATCCGAAGCACAACTTTCCAACAAAGCCAAAT
66 CTTTATAACACCAAATCCGAAGCACAACTTTCCAACAAAGCCAAAT
1850093 CCCGTCTTCCCACGCAACGTTGTAGCTCATCTCTTCAAACTCCTAATCCTGCTGAATGTCTCAAT
1 CCCGTCTTCCCACGCAACGTTGTAGCTCATCTCTTCAAACTCCTAATCCTGCTGAATGTCTCAAT
1850158 CTTTATAACACCAAATCCGAAGCACAACTTTCCAACAAAGCCAAAT
66 CTTTATAACACCAAATCCGAAGCACAACTTTCCAACAAAGCCAAAT
1850204 CC
1 CC
1850206 TGCAGACTCC
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 113 1.00
ACGTcount: A:0.30, C:0.34, G:0.10, T:0.26
Consensus pattern (111 bp):
CCCGTCTTCCCACGCAACGTTGTAGCTCATCTCTTCAAACTCCTAATCCTGCTGAATGTCTCAAT
CTTTATAACACCAAATCCGAAGCACAACTTTCCAACAAAGCCAAAT
Found at i:1867802 original size:2 final size:2
Alignment explanation
Indices: 1867795--1867845 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1867785 TAACTTTAAT
1867795 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
1867837 TA TA TA TA T
1 TA TA TA TA T
1867846 GTGTGTGTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1868245 original size:42 final size:41
Alignment explanation
Indices: 1868193--1868480 Score: 418
Period size: 42 Copynumber: 6.9 Consensus size: 41
1868183 GATTTACATA
* * *
1868193 TTCGCATTGCGA-TAATCCAAGTTCGCGTTGCGATAGTTGAAG
1 TTCGCGTTGCGATTATTCCAAGTT--CGTTGCGATAGTCGAAG
*
1868235 TTCGCGTTGCGATT-TTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAGTTCGTTGCGATAGTCGAAG
*
1868275 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAG
*
1868317 TTCGCGTTGCGATTTATTCAAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAG
* *
1868359 TTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAG
*
1868401 TTCGCTTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAG
1868443 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTC
1868481 CAAAATCGCA
Statistics
Matches: 231, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
40 28 0.12
41 2 0.01
42 200 0.87
43 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (41 bp):
TTCGCGTTGCGATTATTCCAAGTTCGTTGCGATAGTCGAAG
Found at i:1868490 original size:126 final size:124
Alignment explanation
Indices: 1868208--1868480 Score: 465
Period size: 126 Copynumber: 2.2 Consensus size: 124
1868198 ATTGCGATAA
* *
1868208 TCCAAGTTCGCGTTGCGATAGTTGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGA
1 TCCAAGTT--CGTTGCGATAGTCGAAGTTCGCATTGCGATTTTCCAAATTCGTTGCGATAGTCGA
1868273 AGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
64 AGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
1868334 TCAAAGTTCGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCATTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGA
* *
1868399 AGTTCGCTTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
64 AGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1868460 TCCAAGTTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
1868481 CAAAATCGCA
Statistics
Matches: 139, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
124 27 0.19
125 2 0.01
126 110 0.79
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (124 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCATTGCGATTTTCCAAATTCGTTGCGATAGTCGAAG
TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:1868614 original size:21 final size:21
Alignment explanation
Indices: 1868588--1868630 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1868578 GACCACGACC
*
1868588 ACGCGATTTTGGACAAATGCA
1 ACGCGATTTTAGACAAATGCA
1868609 ACGCGATTTTAGACAAATGCA
1 ACGCGATTTTAGACAAATGCA
1868630 A
1 A
1868631 TACCACCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (21 bp):
ACGCGATTTTAGACAAATGCA
Found at i:1868694 original size:23 final size:21
Alignment explanation
Indices: 1868664--1868871 Score: 129
Period size: 21 Copynumber: 10.0 Consensus size: 21
1868654 GACTATCGCA
1868664 ACGAATTTGGAATAAATCGCAAC
1 ACGAATTTGG-A-AAATCGCAAC
*
1868687 ACGAATTTGGAAAATCGTAAC
1 ACGAATTTGGAAAATCGCAAC
1868708 ACGAATTTGGAAAATCGCAAC
1 ACGAATTTGGAAAATCGCAAC
* * * **
1868729 GCGAACTTCGACTATCGC-A-
1 ACGAATTTGGAAAATCGCAAC
* *
1868748 ACGAATTTGAAAAATCGCAAT
1 ACGAATTTGGAAAATCGCAAC
* * * **
1868769 GCGAACTTCGACTATCGC-A-
1 ACGAATTTGGAAAATCGCAAC
1868788 ACGAATTTGGAAAATCGCAAC
1 ACGAATTTGGAAAATCGCAAC
* **
1868809 GCGAACTTT-GACTATCGCAAC
1 ACGAA-TTTGGAAAATCGCAAC
* * * **
1868830 GCGAACTTCGACTATCGCAAC
1 ACGAATTTGGAAAATCGCAAC
* * **
1868851 GCGAACTTGGACTATCGCAAC
1 ACGAATTTGGAAAATCGCAAC
1868872 GAATATGTAA
Statistics
Matches: 150, Mismatches: 29, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
19 25 0.17
20 6 0.04
21 105 0.70
22 4 0.03
23 10 0.07
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (21 bp):
ACGAATTTGGAAAATCGCAAC
Found at i:1868762 original size:40 final size:40
Alignment explanation
Indices: 1868654--1868875 Score: 248
Period size: 40 Copynumber: 5.4 Consensus size: 40
1868644 TGCGATTTTG
* * *
1868654 GACTATCGCAACGAATTTGGAATAAATCGCAACACGAATTTG
1 GACTATCGCAACGAATTT-GAA-AAATCGCAACGCGAACTTC
** * *
1868696 GAAAATCGTAACACGAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCG-CA-ACGAATTTGAAAAATCGCAACGCGAACTTC
*
1868738 GACTATCGCAACGAATTTGAAAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTTC
* *
1868778 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTTC
* ** *
1868818 GACTATCGCAACGCGAACTTCG-ACTATCGCAACGCGAACTTG
1 GACTATCGCAA--CGAA-TTTGAAAAATCGCAACGCGAACTTC
1868860 GACTATCGCAACGAAT
1 GACTATCGCAACGAAT
1868876 ATGTAAATCG
Statistics
Matches: 156, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.01
40 80 0.51
41 1 0.01
42 60 0.38
43 6 0.04
44 8 0.05
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (40 bp):
GACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTTC
Found at i:1868786 original size:61 final size:60
Alignment explanation
Indices: 1868721--1868893 Score: 206
Period size: 61 Copynumber: 2.9 Consensus size: 60
1868711 AATTTGGAAA
*
1868721 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAAATCGCAATGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTG-AAAATCGCAATGCGAACTTCGACT
* ** ** *
1868782 ATCGCAA--CGAATTTGGAAAATCGCAACGCGAACTTTGACTATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAA--CGAA-TTTGAAAATCGCAATGCGAACTTCGACT
* * *
1868843 ATCGCAACGCGAACTTGGACTATCGCAACGAATATGTAAATCGCATTGCGA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAAATCGCAATGCGA
1868894 TAGTCCAAGT
Statistics
Matches: 91, Mismatches: 16, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
59 15 0.16
60 13 0.14
61 43 0.47
62 4 0.04
63 16 0.18
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (60 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAAATCGCAATGCGAACTTCGACT
Found at i:1868825 original size:21 final size:21
Alignment explanation
Indices: 1868721--1868872 Score: 170
Period size: 21 Copynumber: 7.4 Consensus size: 21
1868711 AATTTGGAAA
1868721 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* **
1868742 ATCGCAA--CGAA-TTTGAAAA
1 ATCGCAACGCGAACTTCG-ACT
*
1868761 ATCGCAATGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
1868782 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
1868801 ATCGCAACGCGAACTTTGACT
1 ATCGCAACGCGAACTTCGACT
1868822 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
1868843 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
1868864 ATCGCAACG
1 ATCGCAACG
1868873 AATATGTAAA
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
18 3 0.03
19 27 0.25
21 76 0.70
22 3 0.03
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:1868864 original size:122 final size:123
Alignment explanation
Indices: 1868654--1868893 Score: 324
Period size: 122 Copynumber: 2.0 Consensus size: 123
1868644 TGCGATTTTG
* * *
1868654 GACTATCGCAACGAATTTGGAATAAATCGCAACACGAATTTGGAAAATCGTAACACGAATTTGGA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACACGAATTTGGAAAATCGCAACACGAACTTCGA
*
1868719 AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAAATCGCAATGCGAACTTC
66 AAATCGCAACGCGAACTTCGACTATCGCAACGAATATG-AAAATCGCAATGCGAACTTC
* ** *
1868778 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTT-GACTATCGCAACGCGAACTTCG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACACGAA-TTTGGAAAATCGCAACACGAACTTCG
** * * *
1868840 ACTATCGCAACGCGAACTTGGACTATCGCAACGAATATGTAAATCGCATTGCGA
65 AAAATCGCAACGCGAACTTCGACTATCGCAACGAATATGAAAATCGCAATGCGA
1868894 TAGTCCAAGT
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
121 13 0.13
122 65 0.64
123 4 0.04
124 20 0.20
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (123 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACACGAATTTGGAAAATCGCAACACGAACTTCGA
AAATCGCAACGCGAACTTCGACTATCGCAACGAATATGAAAATCGCAATGCGAACTTC
Found at i:1871181 original size:3 final size:3
Alignment explanation
Indices: 1871175--1871208 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1871165 AAAAAAAGTA
1871175 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1871209 GTTGTTGTGT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1871519 original size:26 final size:29
Alignment explanation
Indices: 1871456--1871517 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
1871446 AATAAATCTT
1871456 ATATTATAATCACTTTAAATTATTAAAAA
1 ATATTATAATCACTTTAAATTATTAAAAA
1871485 ATATTATAATCACTTTAAATTATTAAAAA
1 ATATTATAATCACTTTAAATTATTAAAAA
1871514 ATAT
1 ATAT
1871518 AACAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATTATAATCACTTTAAATTATTAAAAA
Found at i:1872439 original size:43 final size:43
Alignment explanation
Indices: 1872291--1872440 Score: 176
Period size: 43 Copynumber: 3.5 Consensus size: 43
1872281 GCCGTAAATG
* * * * * *
1872291 TCATTTTATATAGCGGCATTTTTCTCCCAAACTCCTCAAAATA
1 TCATGTTATATAGTGGCGTTTTTATCCCAAACGCCTCAAAAGA
* * * * *
1872334 TCATGTTATACAGTGGC-TTTTTATCTCAAACGTCACAAAAGG
1 TCATGTTATATAGTGGCGTTTTTATCCCAAACGCCTCAAAAGA
*
1872376 TTATGTTATATAGTGGCGTTTTTATCCCAAACGCCTCAAAAGA
1 TCATGTTATATAGTGGCGTTTTTATCCCAAACGCCTCAAAAGA
*
1872419 TCATGTTATATAGTGTCGTTTT
1 TCATGTTATATAGTGGCGTTTT
1872441 CACTACAACG
Statistics
Matches: 88, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 33 0.38
43 55 0.62
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (43 bp):
TCATGTTATATAGTGGCGTTTTTATCCCAAACGCCTCAAAAGA
Found at i:1878682 original size:37 final size:37
Alignment explanation
Indices: 1878627--1878719 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
1878617 TTCGTCATAT
* * * *
1878627 TAGGATTCAAATTTCTAAAAATAGGATAAAATTTTGC
1 TAGGATTTAAACTCCTAAAAATAGGATAAAATTTTAC
* *
1878664 TAGGATTTAAACTCCTAAAAATAGGATAGAGTTTTAC
1 TAGGATTTAAACTCCTAAAAATAGGATAAAATTTTAC
**
1878701 TATTATTTAAACTCCTAAA
1 TAGGATTTAAACTCCTAAA
1878720 GATATGATCC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (37 bp):
TAGGATTTAAACTCCTAAAAATAGGATAAAATTTTAC
Found at i:1879676 original size:20 final size:19
Alignment explanation
Indices: 1879652--1879708 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
1879642 TTTTATCTTC
1879652 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
* *
1879671 ATTTTATTTTTTTTTCATCCA
1 A-TTTATTTTATTTT-ATTCA
1879692 A-TTATTTTATATTTATT
1 ATTTATTTTAT-TTTATT
1879709 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 11 0.35
20 15 0.48
21 5 0.16
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:1884019 original size:14 final size:15
Alignment explanation
Indices: 1884002--1884041 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1883992 AACAAAAATG
1884002 GCAAAAAAAAAG-AA
1 GCAAAAAAAAAGAAA
*
1884016 GCAAAAAAGAAGAAA
1 GCAAAAAAAAAGAAA
1884031 GCAAAAAAAAA
1 GCAAAAAAAAA
1884042 AAGAAAGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (15 bp):
GCAAAAAAAAAGAAA
Found at i:1884699 original size:22 final size:22
Alignment explanation
Indices: 1884671--1884725 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1884661 GCTACCCCAT
1884671 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
1884693 CAAACCTTTCAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
1884715 CAAACCTTTGA
1 CAAACCTTTGA
1884726 CCAAACACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.29, G:0.11, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:1886751 original size:106 final size:106
Alignment explanation
Indices: 1885687--1886750 Score: 1633
Period size: 106 Copynumber: 10.0 Consensus size: 106
1885677 ATATCGTGCC
* * * *
1885687 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
1885752 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGACATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1885793 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1885858 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1885899 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1885964 ATTTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1886005 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1886070 AATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1886111 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAACAAATTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1886176 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
1886217 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGAATCGCTGGTTGTCAATAAAGAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
1886282 AATTTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1886323 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1886388 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1886429 ACTCCAGATAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1886494 AATTTCAGAGCTAATTTCAACTGCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** * *
1886535 ACTCGGGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** *
1886600 AATTTTGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
1886641 ACTCGAGACAACACAAGTTCAACTTCACAACTAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
1886706 GATTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1886747 ACTC
1 ACTC
1886751 GGAACAATGC
Statistics
Matches: 880, Mismatches: 78, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 880 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:1887552 original size:37 final size:37
Alignment explanation
Indices: 1887500--1887603 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
1887490 CTTTTCGTCC
*
1887500 TACTAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
1887537 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
** * *
1887574 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
1887604 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:1888195 original size:31 final size:31
Alignment explanation
Indices: 1888155--1888239 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 31
1888145 TATTTTCCTA
*
1888155 TTATATATATATATATTATTATTATTATTTT-
1 TTATCTATATATATATTATTATTA-TATTTTC
1888186 TTATCTATAT-T-TACTTATTTATTATATTTTC
1 TTATCTATATATATA-TTA-TTATTATATTTTC
*
1888217 TTAACGTTATATATATATATATT
1 TTATC--TATATATATAT-TATT
1888240 CTTACTTCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
29 2 0.05
30 10 0.23
31 19 0.43
33 5 0.11
34 4 0.09
35 4 0.09
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (31 bp):
TTATCTATATATATATTATTATTATATTTTC
Found at i:1888213 original size:17 final size:18
Alignment explanation
Indices: 1888185--1888219 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1888175 ATTATTATTT
1888185 TTTATCTATATTTACTTA
1 TTTATCTATATTTACTTA
*
1888203 TTTAT-TATATTTTCTTA
1 TTTATCTATATTTACTTA
1888220 ACGTTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTATCTATATTTACTTA
Found at i:1888570 original size:20 final size:19
Alignment explanation
Indices: 1888521--1888570 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
1888511 TTATCTTCAT
*
1888521 TTATTTTAT-TTTATTCAA
1 TTATTTTATGTTTATCCAA
*
1888539 TT-TGTTTTTGTTTCATCCAA
1 TTAT-TTTATGTTT-ATCCAA
1888559 TTATTTTATGTT
1 TTATTTTATGTT
1888571 CATTATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
17 1 0.04
18 6 0.24
19 3 0.12
20 14 0.56
21 1 0.04
ACGTcount: A:0.20, C:0.08, G:0.06, T:0.66
Consensus pattern (19 bp):
TTATTTTATGTTTATCCAA
Found at i:1893005 original size:23 final size:22
Alignment explanation
Indices: 1892974--1893016 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1892964 TTATCATTTA
*
1892974 TATTTTTTTTATCTATTTAATC
1 TATTTTTTTTATATATTTAATC
*
1892996 TATTTATTTTTTTATATTTAA
1 TATTT-TTTTTATATATTTAA
1893017 ATTTTTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTTTTTTATATATTTAATC
Found at i:1893121 original size:2 final size:2
Alignment explanation
Indices: 1893114--1893171 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1893104 TTCTAATAGC
1893114 AT AT AT AT AT 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 AT AT AT AT AT
1893156 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1893172 GGAGAGAGAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1896418 original size:2 final size:2
Alignment explanation
Indices: 1896411--1896439 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1896401 TACACTTTCA
1896411 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 A
1896440 AAAGAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1898097 original size:17 final size:17
Alignment explanation
Indices: 1898077--1898109 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1898067 GAATTAGAAT
1898077 TAAATTAATAAA-ATAAG
1 TAAA-TAATAAAGATAAG
1898094 TAAATAATAAAGATAA
1 TAAATAATAAAGATAA
1898110 AATGTGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (17 bp):
TAAATAATAAAGATAAG
Found at i:1915357 original size:16 final size:16
Alignment explanation
Indices: 1915336--1915367 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1915326 AATTATACTA
1915336 ATGAATGTGTCGATCC
1 ATGAATGTGTCGATCC
1915352 ATGAATGTGTCGATCC
1 ATGAATGTGTCGATCC
1915368 TCCAAGTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (16 bp):
ATGAATGTGTCGATCC
Found at i:1916323 original size:32 final size:31
Alignment explanation
Indices: 1916205--1916327 Score: 119
Period size: 31 Copynumber: 3.9 Consensus size: 31
1916195 TCCTCGGCAA
* * **
1916205 CTGTCCATAGGTTCCGAAGAACCGAGGTGAA-
1 CTGTCCATATGTTCCGTAGAACATAGGT-AAT
*
1916236 CTGTCCATATGTTCCTTAGAACATAGGT-AT
1 CTGTCCATATGTTCCGTAGAACATAGGTAAT
*
1916266 ACTGTCCATATG-TCTCG-AAAGACATAGGTAATT
1 -CTGTCCATATGTTC-CGTAGA-ACATAGGTAA-T
1916299 CTGTCCATATGTTCCGTAGAACATAGGTA
1 CTGTCCATATGTTCCGTAGAACATAGGTA
1916328 CCCTCGACTC
Statistics
Matches: 76, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
29 1 0.01
30 4 0.05
31 43 0.57
32 23 0.30
33 5 0.07
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (31 bp):
CTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:1917080 original size:64 final size:64
Alignment explanation
Indices: 1916975--1917195 Score: 236
Period size: 64 Copynumber: 3.5 Consensus size: 64
1916965 TAATGAAGGA
* * ** *
1916975 ATGCATCGATGCACTA-CTGATGCATCGGTGCA-TAAAATGCATTCGATGTTTGTTTATTACTGG
1 ATGCATCGATGCACTACCT-ATGCATCGATGCACT-AATTGCATTCGATGTTTCCTTATTAATGG
1917038 G
64 G
*
1917039 ATGCATCGATGCA-TGCCCTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACCTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
* * * ** **
1917103 ATGCATCGATGCACTACTTATGCATTGATGCACGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACCTATGCATCGATGCACTAATTGCATTCGATGT-TTCCTTATTAATGGG
*
1917166 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACCTATGCATCGAT
1917196 ACACCTTCAA
Statistics
Matches: 134, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
63 3 0.02
64 123 0.92
65 8 0.06
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
Found at i:1921518 original size:30 final size:30
Alignment explanation
Indices: 1921478--1921549 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
1921468 CCCGCAGGAC
*
1921478 CTATCCAGAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCATCGGCAA
* *
1921508 CTATCTAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCATCGGCAA
* *
1921538 CTGTCCATAGGT
1 CTATCCAGAGGT
1921550 TCCGAAGAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCATCGGCAA
Found at i:1921574 original size:31 final size:30
Alignment explanation
Indices: 1921536--1921660 Score: 110
Period size: 31 Copynumber: 4.0 Consensus size: 30
1921526 GATCCTCGGC
*
1921536 AACTGTCCATAGGTTCCGAAGAACCTAGGT
1 AACTGTCCATAGGTTCCGAAGAACATAGGT
* **
1921566 GAACTGTCCATATGTTCCTTAGAACATAGGT
1 -AACTGTCCATAGGTTCCGAAGAACATAGGT
* *
1921597 ATACTGTCCATATG-TCTCGAA-AGATATAGGT
1 A-ACTGTCCATAGGTTC-CGAAGA-ACATAGGT
* *
1921628 AATTCTGTCCATATGTTCCGTAGAACATAGGT
1 AA--CTGTCCATAGGTTCCGAAGAACATAGGT
1921660 A
1 A
1921661 CCCTCGACTC
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
30 5 0.06
31 48 0.62
32 22 0.28
33 3 0.04
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (30 bp):
AACTGTCCATAGGTTCCGAAGAACATAGGT
Found at i:1922413 original size:64 final size:64
Alignment explanation
Indices: 1922308--1922528 Score: 252
Period size: 64 Copynumber: 3.5 Consensus size: 64
1922298 TAATGAAGGT
* * * ** *
1922308 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCCTTATTAATGGG
*
1922372 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCCTTATTAATGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCA-TAAATTGCATTCGATGTTTCCTTATTAATGG
1922435 G
64 G
* ** **
1922436 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTCCTTATTAATGGG
**
1922499 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
1922529 ACACCTTCAA
Statistics
Matches: 137, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
63 4 0.03
64 127 0.93
65 6 0.04
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCCTTATTAATGGG
Found at i:1923785 original size:36 final size:36
Alignment explanation
Indices: 1923720--1923789 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
1923710 CCTTAGGCCC
*
1923720 ATAAGGAATTACCAGCTTGATCAGTGTTGAACCTAT
1 ATAAGGAATTACCAGCTTGATCAGAGTTGAACCTAT
*
1923756 ATAAGGAATTATCAGCTTGATC-GAAGTTGAACCT
1 ATAAGGAATTACCAGCTTGATCAG-AGTTGAACCT
1923790 GCAGAGACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (36 bp):
ATAAGGAATTACCAGCTTGATCAGAGTTGAACCTAT
Found at i:1926692 original size:21 final size:21
Alignment explanation
Indices: 1926625--1926704 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
1926615 TTTTCGTAAG
* *
1926625 AGTACTTTTTATACTTAGAGT
1 AGTACTTTGTGTACTTAGAGT
* * *
1926646 AGTACTTTTTGTACTATGGCAAT
1 AGTACTTTGTGTACT-TAG-AGT
1926669 AGTACTTTGTGTACTT-GTAGT
1 AGTACTTTGTGTACTTAG-AGT
*
1926690 AGTAGTTTGTGTACT
1 AGTACTTTGTGTACT
1926705 ATGACACTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 31 0.62
22 3 0.06
23 16 0.32
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (21 bp):
AGTACTTTGTGTACTTAGAGT
Found at i:1927261 original size:2 final size:2
Alignment explanation
Indices: 1927254--1927279 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1927244 ATGGATTTTA
1927254 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
1927280 TGAAGAATAT
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):
AT
Found at i:1927490 original size:20 final size:20
Alignment explanation
Indices: 1927465--1927502 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1927455 TTAACGGTCA
*
1927465 GGTCAAATTCAACGGGTCTG
1 GGTCAAAGTCAACGGGTCTG
1927485 GGTCAAAGTCAACGGGTC
1 GGTCAAAGTCAACGGGTC
1927503 AGAGCGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (20 bp):
GGTCAAAGTCAACGGGTCTG
Found at i:1928378 original size:23 final size:23
Alignment explanation
Indices: 1928315--1928380 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
1928305 CTGAATGATT
*
1928315 CAGTGCTGACTGATTCAACAAAA
1 CAGTGCTGACTGATTCAGCAAAA
*
1928338 TAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
* *
1928361 CAGTACTGAATGATTCAGCA
1 CAGTGCTGACTGATTCAGCA
1928381 GAGAAGTACA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (23 bp):
CAGTGCTGACTGATTCAGCAAAA
Found at i:1942712 original size:16 final size:16
Alignment explanation
Indices: 1942691--1942727 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1942681 CTTTTGGAAT
1942691 AGTAATA-TGAATATGA
1 AGTAATAGT-AATATGA
1942707 AGTAATAGTAATATGA
1 AGTAATAGTAATATGA
1942723 AGTAA
1 AGTAA
1942728 AACCCAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (16 bp):
AGTAATAGTAATATGA
Found at i:1943231 original size:212 final size:212
Alignment explanation
Indices: 1942823--1943246 Score: 823
Period size: 212 Copynumber: 2.0 Consensus size: 212
1942813 GTAAAATTTT
1942823 AATATAAAACTGCTATTTTGTTGGGAACCACTTCCGACAAAGTCACGGGAAATTCTCTTTCCGAG
1 AATATAAAACTGCTATTTTGTTGGGAACCACTTCCGACAAAGTCACGGGAAATTCTCTTTCCGAG
1942888 CCTTTTGTTTTTTAAAAAGAAAAATGGAATGTTAATGAAAACGCGCCGGGTGAACTAACGTCTAC
66 CCTTTTGTTTTTTAAAAAGAAAAATGGAATGTTAATGAAAACGCGCCGGGTGAACTAACGTCTAC
1942953 CGTCTTAATCTGACGTGTCAACGGATTTAACTAAAGTACGCCTCATTTCAGACAGCGTTGTGGAC
131 CGTCTTAATCTGACGTGTCAACGGATTTAACTAAAGTACGCCTCATTTCAGACAGCGTTGTGGAC
1943018 GACACGAGGGGGGGAAA
196 GACACGAGGGGGGGAAA
*
1943035 AATATAAAACTGCTATTTTGTTGGGAACCACTTCCGACAAAGTCACGGGAAATTTTCTTTCCGAG
1 AATATAAAACTGCTATTTTGTTGGGAACCACTTCCGACAAAGTCACGGGAAATTCTCTTTCCGAG
1943100 CCTTTTGTTTTTTAAAAAGAAAAATGGAATGTTAATGAAAACGCGCCGGGTGAACTAACGTCTAC
66 CCTTTTGTTTTTTAAAAAGAAAAATGGAATGTTAATGAAAACGCGCCGGGTGAACTAACGTCTAC
1943165 CGTCTATAATCTGACGTGTCAACGGATTTAACTAAAGTACGCCTCATTTCAGACAGCGTT-TGGA
131 CGTCT-TAATCTGACGTGTCAACGGATTTAACTAAAGTACGCCTCATTTCAGACAGCGTTGTGGA
1943229 CGACACGAGGGGGGGAAA
195 CGACACGAGGGGGGGAAA
1943247 CTGCATGGAA
Statistics
Matches: 210, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
212 156 0.74
213 54 0.26
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (212 bp):
AATATAAAACTGCTATTTTGTTGGGAACCACTTCCGACAAAGTCACGGGAAATTCTCTTTCCGAG
CCTTTTGTTTTTTAAAAAGAAAAATGGAATGTTAATGAAAACGCGCCGGGTGAACTAACGTCTAC
CGTCTTAATCTGACGTGTCAACGGATTTAACTAAAGTACGCCTCATTTCAGACAGCGTTGTGGAC
GACACGAGGGGGGGAAA
Found at i:1947012 original size:14 final size:14
Alignment explanation
Indices: 1946991--1947050 Score: 54
Period size: 15 Copynumber: 4.3 Consensus size: 14
1946981 ATTATTTTTA
1946991 TATT-AATA-TATT
1 TATTAAATATTATT
1947003 TATGTAAATATTATTT
1 TAT-TAAATATTA-TT
*
1947019 TATTAAA-AATATT
1 TATTAAATATTATT
*
1947032 TATATAATTATTATT
1 TAT-TAAATATTATT
1947047 TATT
1 TATT
1947051 TAGAATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
12 3 0.08
13 6 0.15
14 11 0.28
15 14 0.36
16 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TATTAAATATTATT
Found at i:1947043 original size:29 final size:30
Alignment explanation
Indices: 1946970--1947047 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
1946960 GTTAGTATTT
* * * *
1946970 TTTAAATAGTTATTATTTTTATATTAATATA
1 TTTATATAATTATTA-TTTTATATAAAAATA
* *
1947001 TTTATGTAAATATTATTTTAT-TAAAAATA
1 TTTATATAATTATTATTTTATATAAAAATA
1947030 TTTATATAATTATTATTT
1 TTTATATAATTATTATTT
1947048 ATTTAGAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 22 0.56
30 6 0.15
31 11 0.28
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
TTTATATAATTATTATTTTATATAAAAATA
Found at i:1947048 original size:15 final size:15
Alignment explanation
Indices: 1946965--1947049 Score: 50
Period size: 15 Copynumber: 5.7 Consensus size: 15
1946955 TTTATGTTAG
* * *
1946965 TATTTTTTAAATAGT
1 TATTATTTATATAAT
*
1946980 TATTATTTTTAT-AT
1 TATTATTTATATAAT
* *
1946994 TAATATATTTATGTAAA
1 T-AT-TATTTATATAAT
1947011 TATTATTT-TATTAA-
1 TATTATTTATA-TAAT
* *
1947025 AAATATTTATATAAT
1 TATTATTTATATAAT
1947040 TATTATTTAT
1 TATTATTTAT
1947050 TTAGAATTAT
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
14 12 0.23
15 29 0.56
16 9 0.17
17 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TATTATTTATATAAT
Found at i:1947060 original size:29 final size:29
Alignment explanation
Indices: 1946999--1947060 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1946989 TATATTAATA
* * * *
1946999 TATTTATGTAAATATTATTTTATTAAAAA
1 TATTTATATAATTATTATTTTATTAGAAT
1947028 TATTTATATAATTATTA-TTTATTTAGAAT
1 TATTTATATAATTATTATTTTA-TTAGAAT
1947057 TATT
1 TATT
1947061 AATTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
TATTTATATAATTATTATTTTATTAGAAT
Found at i:1947209 original size:17 final size:17
Alignment explanation
Indices: 1947189--1947242 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1947179 AATGTTAATA
1947189 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1947206 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1947223 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1947240 TTT
1 TTT
1947243 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1952893 original size:20 final size:21
Alignment explanation
Indices: 1952868--1952919 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1952858 TTTTCCCAAT
*
1952868 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1952888 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1952909 TCGCAATGCGA
1 TCGCAATGCGA
1952920 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1952933 original size:20 final size:20
Alignment explanation
Indices: 1952908--1953021 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
1952898 AATTGGGAAA
1952908 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1952928 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1952948 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1952969 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
1952989 TTCGCAATGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
1953009 TTCGCAACGCGAT
1 ATCGCAATGCGAT
1953022 TTACACAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1952952 original size:61 final size:61
Alignment explanation
Indices: 1952905--1953021 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
1952895 GCGAATTGGG
* * * *
1952905 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* * *
1952966 AAAATCGCAACGAGATACTGACTTTCGCAATGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAATGCGATACTGACTATCGCAACGCGAT
1953022 TTACACAGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1953578 original size:19 final size:19
Alignment explanation
Indices: 1953540--1953606 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1953530 TTCGAGAATG
1953540 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1953560 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1953579 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1953598 AAAATCGCA
1 AAAATCGCA
1953607 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1953624 original size:19 final size:19
Alignment explanation
Indices: 1953602--1953772 Score: 172
Period size: 19 Copynumber: 9.1 Consensus size: 19
1953592 GAAACCAAAA
*
1953602 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1953621 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1953640 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1953659 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1953679 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1953695 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
1953712 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
1953731 TCCGCATTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
1953751 ATCTCGTTGCGATTTTTATT
1 -TCGCGTTGCGATTTTCATT
1953771 TC
1 TC
1953773 AACCAAAAGA
Statistics
Matches: 130, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
14 10 0.08
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 68 0.52
20 47 0.36
21 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1953679 original size:39 final size:38
Alignment explanation
Indices: 1953602--1953772 Score: 172
Period size: 39 Copynumber: 4.6 Consensus size: 38
1953592 GAAACCAAAA
*
1953602 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
1953640 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
1953679 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
** * *
1953712 TCGCGTTGCGATAGTCATTTCCGCATTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTT-CGCGTTGCGATTTTCATT
* *
1953751 ATCTCGTTGCGATTTTTATTTC
1 -TCGCGTTGCGATTTTCATTTC
1953773 AACCAAAAGA
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
33 27 0.25
35 1 0.01
36 2 0.02
38 22 0.20
39 41 0.38
40 16 0.15
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:1953749 original size:20 final size:19
Alignment explanation
Indices: 1953700--1953750 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1953690 TTGTCTGGTC
* *
1953700 GCGATAGTCATTTCGCGTT
1 GCGATACTCATTTCGCATT
*
1953719 GCGATAGTCATTTCCGCATT
1 GCGATACTCATTT-CGCATT
*
1953739 GCGATTCTCATT
1 GCGATACTCATT
1953751 ATCTCGTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.37
Consensus pattern (19 bp):
GCGATACTCATTTCGCATT
Found at i:1955832 original size:42 final size:42
Alignment explanation
Indices: 1955772--1955892 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 42
1955762 GCCCGACTCG
* * *
1955772 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1955814 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1955856 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAG
1955893 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 60 0.94
43 4 0.06
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1955852 original size:21 final size:21
Alignment explanation
Indices: 1955828--1955892 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
1955818 TCATTCCTCG
1955828 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1955849 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1955870 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1955891 AG
1 AG
1955893 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 13, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.23, C:0.37, G:0.20, T:0.20
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1957258 original size:14 final size:14
Alignment explanation
Indices: 1957239--1957274 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1957229 ATTGTTTAAT
1957239 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1957253 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1957267 TGATTTGT
1 TGATTTGT
1957275 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1957456 original size:19 final size:20
Alignment explanation
Indices: 1957409--1957446 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1957399 ATCGCAACGA
*
1957409 GAAAATCGTAACGCGAAAAT
1 GAAAATCGCAACGCGAAAAT
1957429 GAAAATCGCAACGCGAAA
1 GAAAATCGCAACGCGAAA
1957447 TTAAATTCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.21, T:0.11
Consensus pattern (20 bp):
GAAAATCGCAACGCGAAAAT
Found at i:1957474 original size:19 final size:19
Alignment explanation
Indices: 1957452--1957602 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
1957442 CGAAATTAAA
1957452 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1957471 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1957486 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1957504 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1957518 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1957537 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1957552 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1957570 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1957589 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1957603 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1957498 original size:33 final size:32
Alignment explanation
Indices: 1957456--1957582 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
1957446 ATTAAATTCG
1957456 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1957489 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1957522 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1957555 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1957583 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1957545 original size:66 final size:66
Alignment explanation
Indices: 1957449--1957581 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1957439 ACGCGAAATT
*
1957449 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1957514 G
66 G
*
1957515 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1957580 G
66 G
1957581 A
1 A
1957582 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1960098 original size:24 final size:23
Alignment explanation
Indices: 1960060--1960113 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
1960050 CTGAAACATC
* *
1960060 ATCAAATCCGTGTATTGACCAAT
1 ATCAAATCCGGGTATTGACCAAG
1960083 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAA-TCCGGGTATTGACCAAG
1960107 ATCAAAT
1 ATCAAAT
1960114 TTCGAATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (23 bp):
ATCAAATCCGGGTATTGACCAAG
Found at i:1961219 original size:20 final size:20
Alignment explanation
Indices: 1961162--1961237 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
1961152 ATTCATTTGA
1961162 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1961182 CT-TCGCAATGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
1961200 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1961220 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1961238 CGCAATGCGA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 8 0.16
19 18 0.35
20 25 0.49
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1961280 original size:14 final size:15
Alignment explanation
Indices: 1961260--1961331 Score: 58
Period size: 18 Copynumber: 4.5 Consensus size: 15
1961250 TGAAAATCGC
1961260 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
1961275 -TTGCGATTTTCATTCG
1 ATTGCGATTTTC--TCG
*
1961291 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
*
1961309 CATTGCGATTTTCTTG
1 -ATTGCGATTTTCTCG
1961325 -TTGCGAT
1 ATTGCGAT
1961332 AGCCATTTCG
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
14 18 0.38
16 6 0.12
18 23 0.48
20 1 0.02
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:1961298 original size:18 final size:18
Alignment explanation
Indices: 1961256--1961321 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
1961246 GAAATGAAAA
1961256 TCGCATTGCGATTTTC--
1 TCGCATTGCGATTTTCAT
1961272 TCG--TTGCGATTTTCAT
1 TCGCATTGCGATTTTCAT
1961288 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCA-T
1961306 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1961322 TTGTTGCGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.25
16 6 0.14
17 5 0.11
18 18 0.41
19 4 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTTCAT
Found at i:1963341 original size:20 final size:19
Alignment explanation
Indices: 1963306--1963372 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1963296 GAAACTTAAA
1963306 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1963325 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1963345 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1963364 ATCGCAACG
1 ATCGCAACG
1963373 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1963418 original size:14 final size:14
Alignment explanation
Indices: 1963401--1963458 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1963391 ACACAAATCG
1963401 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1963415 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1963431 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1963447 CGTTGCGATTTT
1 CGTTGCGATTTT
1963459 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1963439 original size:32 final size:33
Alignment explanation
Indices: 1963398--1963474 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 33
1963388 GAAACACAAA
1963398 TCGCGTTGCGATTTTGTCGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
1963430 TCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
*
1963463 TCGCATTGCGAT
1 TCGCGTTGCGAT
1963475 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 25 0.58
33 18 0.42
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.45
Consensus pattern (33 bp):
TCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
Found at i:1963473 original size:19 final size:17
Alignment explanation
Indices: 1963417--1963474 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
1963407 GATTTTGTCG
1963417 TTGCGATTTCATTTCGC
1 TTGCGATTTCATTTCGC
*
1963434 GTTGCGATTT--TGTCG-
1 -TTGCGATTTCATTTCGC
1963449 TTGCGATTTTCATTTCGC
1 TTGCGA-TTTCATTTCGC
1963467 ATTGCGAT
1 -TTGCGAT
1963475 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
17 4 0.12
18 10 0.30
19 6 0.18
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (17 bp):
TTGCGATTTCATTTCGC
Found at i:1963493 original size:20 final size:19
Alignment explanation
Indices: 1963459--1963513 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1963449 TTGCGATTTT
*
1963459 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1963478 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1963498 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1963514 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1964014 original size:18 final size:18
Alignment explanation
Indices: 1963991--1964030 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1963981 CGATCAGATG
*
1963991 GCTCTGGGTGAGGTGATA
1 GCTCTGGGCGAGGTGATA
*
1964009 GCTCTGGGCGAGGTGATG
1 GCTCTGGGCGAGGTGATA
1964027 GCTC
1 GCTC
1964031 CCGAAGTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.17, G:0.45, T:0.25
Consensus pattern (18 bp):
GCTCTGGGCGAGGTGATA
Found at i:1965375 original size:20 final size:20
Alignment explanation
Indices: 1965350--1965387 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1965340 AATAGTTTCT
1965350 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1965370 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1965388 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1965894 original size:20 final size:20
Alignment explanation
Indices: 1965869--1965962 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1965859 GATTATGTAT
1965869 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1965889 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1965909 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1965930 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1965950 TATCGCATTGCGA
1 TATCGCGTTGCGA
1965963 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1965963 original size:20 final size:20
Alignment explanation
Indices: 1965849--1965963 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1965839 CACTTTGAAA
*
1965849 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1965870 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1965890 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1965910 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1965931 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1965951 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1965964 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1965981 original size:21 final size:21
Alignment explanation
Indices: 1965952--1966044 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
1965942 ATAGTCAGTA
1965952 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1965973 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1965993 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1966014 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1966034 TCGCATTGCGA
1 TCGCATTGCGA
1966045 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1965982 original size:41 final size:41
Alignment explanation
Indices: 1965891--1966025 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1965881 AAAGTCAGTA
* * * ** *
1965891 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
1965931 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1965973 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1966014 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1966026 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1966026 original size:41 final size:41
Alignment explanation
Indices: 1965952--1966044 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1965942 ATAGTCAGTA
1965952 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1965993 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1966034 TCGCATTGCGA
1 TCGCATTGCGA
1966045 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1973844 original size:18 final size:18
Alignment explanation
Indices: 1973823--1973857 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1973813 AACAAATGAT
1973823 ATTATTGTAAAA-AATATA
1 ATTATT-TAAAATAATATA
1973841 ATTATTTAAAATAATAT
1 ATTATTTAAAATAATAT
1973858 CTAAATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTATTTAAAATAATATA
Found at i:1974417 original size:260 final size:254
Alignment explanation
Indices: 1973938--1974450 Score: 956
Period size: 260 Copynumber: 2.0 Consensus size: 254
1973928 ATATTATTCT
1973938 TTTTATAATATATTATATTTTATATAAATAAATATGATACTTATTAAAATTATTTAAAAAATAAG
1 TTTTATAATATATTATATTTTATATAAATAAATATGATACTTATTAAAATTATTTAAAAAATAAG
1974003 TTTGATACTAATTATATTAATTACATGCTAAATTTTTTCTTAAAAGTTAGATAGTGTAACAATTA
66 TTTGATACTAATTATATTAATTACATGCTAAATTTTTTCTTAAAAGTTAGATAGTGTAACAATTA
1974068 AATATTTATATGAATTTTATTCAAATTTTTATTATTGTTTAACTTGCTAAAAAAAACATATATCT
131 AATATTTATATGAATTTTATTCAAATTTTTATTATTGTTTAACTTGCTAAAAAAAACATATATCT
1974133 CAAGGGTAATTTAGTAAAATGTACATTCAAGTAATCTTATATTTTCCCAACCAAATATC
196 CAAGGGTAATTTAGTAAAATGTACATTCAAGTAATCTTATATTTTCCCAACCAAATATC
1974192 TTTTATAATATATTATATTTTATATAAATAAATATGATACTTATTAAAATTATTTAAAAATATAA
1 TTTTATAATATATTATATTTTATATAAATAAATATGATACTTATTAAAATTATTTAAAAA-ATAA
1974257 GTTTGATATACTAATTATATTAATTACATGCTAAATTTTTTTTCTTAAAAGTTAGATAGTGTAAC
65 GTTTG--ATACTAATTATATTAATTACATGCTAAA--TTTTTTCTTAAAAGTTAGATAGTGTAAC
1974322 AATTAAAATATTTATATGAATTTTTATTCAAATTTTTATTATTGTTTAACTTGCT-AAAAAAACA
126 AATT-AAATATTTATATGAA-TTTTATTCAAATTTTTATTATTGTTTAACTTGCTAAAAAAAACA
1974386 TATATCTCAAGGGTAATTTAGTAAAATGTACATTCAAGTAATCTTATATTTTCCCAACCAAATAT
189 TATATCTCAAGGGTAATTTAGTAAAATGTACATTCAAGTAATCTTATATTTTCCCAACCAAATAT
1974451 TGTAAACTTA
Statistics
Matches: 252, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
254 60 0.24
255 9 0.04
257 28 0.11
259 32 0.13
260 89 0.35
261 34 0.13
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.44
Consensus pattern (254 bp):
TTTTATAATATATTATATTTTATATAAATAAATATGATACTTATTAAAATTATTTAAAAAATAAG
TTTGATACTAATTATATTAATTACATGCTAAATTTTTTCTTAAAAGTTAGATAGTGTAACAATTA
AATATTTATATGAATTTTATTCAAATTTTTATTATTGTTTAACTTGCTAAAAAAAACATATATCT
CAAGGGTAATTTAGTAAAATGTACATTCAAGTAATCTTATATTTTCCCAACCAAATATC
Found at i:1987661 original size:145 final size:146
Alignment explanation
Indices: 1987478--1987772 Score: 463
Period size: 146 Copynumber: 2.0 Consensus size: 146
1987468 TGCCACTAAG
* * *
1987478 TTTTTACCGATGGGTATCAAACTGAAATCTAAACT-AA-A-TGTTAGGTATGATTTTAAAAAAAA
1 TTTTTAACGATGGGTATCAAACTGAAACCTAAACTAAATATTATTAGGTATGA-TTT-AAAAAAA
* *
1987540 TAAAATTTAGATATTAAAAT-AGAATAAAAGTGATAATTTAAGTACTAATCATTTAACTTACCCT
64 TAAAATTTAGATATTAAAATGA-AACAAAAGTGATAATTTAAGTACTAAACATTTAACTTACCCT
1987604 AGAAAATATCATGTTCAGA
128 AGAAAATATCATGTTCAGA
1987623 TTTTTAACGATGGGTATCAAACTGAAACCTAAACTAAATATTATTAGGTATGATTTAAAAAAATA
1 TTTTTAACGATGGGTATCAAACTGAAACCTAAACTAAATATTATTAGGTATGATTTAAAAAAATA
* **
1987688 AAATTTAGATATTAAAATGAAACAAAAGTGATAATTTAGGTACTAAACATTTATTTTACCCTAGA
66 AAATTTAGATATTAAAATGAAACAAAAGTGATAATTTAAGTACTAAACATTTAACTTACCCTAGA
1987753 AAATATCATGTTCAGA
131 AAATATCATGTTCAGA
1987769 TTTT
1 TTTT
1987773 AAATTTAAAA
Statistics
Matches: 138, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
145 33 0.24
146 89 0.64
147 5 0.04
148 11 0.08
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (146 bp):
TTTTTAACGATGGGTATCAAACTGAAACCTAAACTAAATATTATTAGGTATGATTTAAAAAAATA
AAATTTAGATATTAAAATGAAACAAAAGTGATAATTTAAGTACTAAACATTTAACTTACCCTAGA
AAATATCATGTTCAGA
Found at i:1997990 original size:35 final size:35
Alignment explanation
Indices: 1997944--1998015 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
1997934 CCAATAAAGA
* * * *
1997944 AGAGTTGGATTAGGACTCAAATATTAGTCTAGAAT
1 AGAGTTGGATTAGAACTCAAATACTAGTATAAAAT
1997979 AGAGTTGGATTAGAACTCAAATACTAGTATAAAAT
1 AGAGTTGGATTAGAACTCAAATACTAGTATAAAAT
1998014 AG
1 AG
1998016 GGTTTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (35 bp):
AGAGTTGGATTAGAACTCAAATACTAGTATAAAAT
Found at i:1998205 original size:21 final size:21
Alignment explanation
Indices: 1998179--1998225 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1998169 ATAATTTCTT
* *
1998179 TTATTTCTTTTTTTACTA-TTA
1 TTATTT-TTATTTTAATACTTA
1998200 TTATTTTTATTTTAATACTTA
1 TTATTTTTATTTTAATACTTA
1998221 TTATT
1 TTATT
1998226 ACTATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (21 bp):
TTATTTTTATTTTAATACTTA
Found at i:1998231 original size:21 final size:20
Alignment explanation
Indices: 1998189--1998231 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1998179 TTATTTCTTT
* **
1998189 TTTTACTATTATTATTTTTA
1 TTTTAATATTATTATTACTA
1998209 TTTTAATACTTATTATTACTA
1 TTTTAATA-TTATTATTACTA
1998230 TT
1 TT
1998232 ATTTTTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTAATATTATTATTACTA
Found at i:1998524 original size:29 final size:28
Alignment explanation
Indices: 1998484--1998543 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
1998474 ATTAGATTCG
*
1998484 TTACTTCATTCTTT-TTTCTTGTTTATTT
1 TTACTTCATTCTTTATTTCTTATTT-TTT
*
1998512 TTACTTTACTTCTTTATTTCTTATTTTTT
1 TTACTTCA-TTCTTTATTTCTTATTTTTT
1998541 TTA
1 TTA
1998544 TCTCATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 12 0.43
30 9 0.32
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (28 bp):
TTACTTCATTCTTTATTTCTTATTTTTT
Found at i:2007622 original size:109 final size:109
Alignment explanation
Indices: 2007431--2007855 Score: 726
Period size: 109 Copynumber: 3.9 Consensus size: 109
2007421 GGGGCCATCC
* *
2007431 GATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTGTCGACA
1 GATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACA
* *
2007496 AACAACTTCCCAATTTCAGAGCCGATTTCAACTCTACAACGAAG
66 AACAACTTCCCAATTTCAGAGCCGATTTCAACTCCACGACGAAG
*
2007540 GATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACA
1 GATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACA
* *
2007605 AAAAACTTCCCAATTTCAGAGCCGATTTCAACTCCACGACGGAG
66 AACAACTTCCCAATTTCAGAGCCGATTTCAACTCCACGACGAAG
*
2007649 GATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGAAAGGACGACTGGTTGTCAACA
1 GATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACA
2007714 AACAACTTCCCAATTTCAGAGCCGATTTCAACTCCACGACGGAA-
66 AACAACTTCCCAATTTCAGAGCCGATTTCAACTCCACGAC-GAAG
* * *
2007758 GATATCGTGTTACCCGAGACAACACAAGTTCAACTTCACAACGAAGGGACAATTGGTTGTCAACA
1 GATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACA
*
2007823 AACAACTTCCCAATTTCAGAGTCGATTTCAACT
66 AACAACTTCCCAATTTCAGAGCCGATTTCAACT
2007856 TGTATTGGAT
Statistics
Matches: 299, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
109 297 0.99
110 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (109 bp):
GATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACA
AACAACTTCCCAATTTCAGAGCCGATTTCAACTCCACGACGAAG
Found at i:2008355 original size:35 final size:35
Alignment explanation
Indices: 2008308--2008379 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
2008298 CCAACAAAGA
*
2008308 AGAGTTGAATTAGGACTCAAATACTAGTCTAGAAT
1 AGAGTTGAATTAGGACTCAAATACTAGTCTAAAAT
*
2008343 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGAATTAGGACTCAAATACTAGTCTAAAAT
2008378 AG
1 AG
2008380 GGTTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (35 bp):
AGAGTTGAATTAGGACTCAAATACTAGTCTAAAAT
Found at i:2008903 original size:2 final size:2
Alignment explanation
Indices: 2008896--2008924 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2008886 TACTTTATTT
2008896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2008925 TTACTTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2009205 original size:15 final size:14
Alignment explanation
Indices: 2009187--2009234 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
2009177 TGTGATTGTT
2009187 TTTTCTTTTCATTTA
1 TTTT-TTTTCATTTA
*
2009202 TTTTTTTTCTTTGTA
1 TTTTTTTTCATT-TA
*
2009217 TTTTTTCTCA-TTA
1 TTTTTTTTCATTTA
2009230 TTTTT
1 TTTTT
2009235 ATTGTTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 7 0.24
14 8 0.28
15 14 0.48
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTTTTTCATTTA
Found at i:2016406 original size:2 final size:2
Alignment explanation
Indices: 2016394--2016424 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2016384 AACAAGTCAG
*
2016394 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2016425 TCATCTTGCT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2019714 original size:2 final size:2
Alignment explanation
Indices: 2019707--2019754 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2019697 ATAACTTTAT
2019707 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
2019749 TA TA TA
1 TA TA TA
2019755 ACACGCACAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2036433 original size:21 final size:21
Alignment explanation
Indices: 2036400--2036476 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
2036390 TGGTGACGGC
*
2036400 GGCGATGGAGTAGATGTAGGA
1 GGCGAAGGAGTAGATGTAGGA
*
2036421 GGCGAAGGGGTAGATGTAGAAGGA
1 GGCGAAGGAGTAGATGT---AGGA
* * *
2036445 GGCGATGGAGTTGAAGTAGGA
1 GGCGAAGGAGTAGATGTAGGA
*
2036466 GGGGAAGGAGT
1 GGCGAAGGAGT
2036477 CGAGGATGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 28 0.62
24 17 0.38
ACGTcount: A:0.30, C:0.04, G:0.51, T:0.16
Consensus pattern (21 bp):
GGCGAAGGAGTAGATGTAGGA
Found at i:2036535 original size:48 final size:48
Alignment explanation
Indices: 2036483--2036595 Score: 145
Period size: 48 Copynumber: 2.4 Consensus size: 48
2036473 GAGTCGAGGA
* * * *
2036483 TGAAGGGGGTGGAGCTGCAGTGGCGGGAGGAGGAGGGGATGGGGTGGT
1 TGAAGGAGGAGGAGCTGCAGTGGAGGGAGGAGGAGCGGATGGGGTGGT
* * ** *
2036531 TGAAGGAGGAGGTGATGGGGTGGAGGGAGGAGGAGCTGATGGGGTGGT
1 TGAAGGAGGAGGAGCTGCAGTGGAGGGAGGAGGAGCGGATGGGGTGGT
2036579 TGAAGGAGGAGGAGCTG
1 TGAAGGAGGAGGAGCTG
2036596 ATGGGGTGGT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.20, C:0.04, G:0.60, T:0.15
Consensus pattern (48 bp):
TGAAGGAGGAGGAGCTGCAGTGGAGGGAGGAGGAGCGGATGGGGTGGT
Done.