Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007768.1 Hibiscus syriacus cultivar Beakdansim tig00110044_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: 2539099
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1686023 original size:15 final size:16
Alignment explanation
Indices: 1685997--1686026 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1685987 TCGAGAAAGG
1685997 TTTGATAATTTAGGGA
1 TTTGATAATTTAGGGA
1686013 TTTGA-AATTTAGGG
1 TTTGATAATTTAGGG
1686027 TTCAAGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (16 bp):
TTTGATAATTTAGGGA
Found at i:1688082 original size:2 final size:2
Alignment explanation
Indices: 1688075--1688103 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1688065 ATAAACTGCA
1688075 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
1688104 AAGACGAATA
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:1689890 original size:20 final size:18
Alignment explanation
Indices: 1689861--1689936 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 18
1689851 CGTTGGACCC
*
1689861 AAAGTATCGAAACTTTAATG
1 AAAGTTTCGAAACTTT--TG
1689881 AAAGTTTCGAAACTTTTG
1 AAAGTTTCGAAACTTTTG
*
1689899 AGATAGTTTCGAAACTATTGG
1 A-A-AGTTTCGAAACT-TTTG
*
1689920 AAA-TTATCAAAACTTTT
1 AAAGTT-TCGAAACTTTT
1689937 CGGAAACTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.15
19 9 0.19
20 28 0.58
21 4 0.08
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (18 bp):
AAAGTTTCGAAACTTTTG
Found at i:1689964 original size:21 final size:21
Alignment explanation
Indices: 1689940--1690011 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
1689930 AACTTTTCGG
*
1689940 AAACTGTCTTG-GAAGGTTTCA
1 AAACT-TCTTGAGAAAGTTTCA
1689961 AAAC-TCTTGTAGAAAGTTTCA
1 AAACTTCTTG-AGAAAGTTTCA
*
1689982 AAAC-TCTTGTA-AAAGTTTCG
1 AAACTTCTTG-AGAAAGTTTCA
1690002 AAACTTCTTG
1 AAACTTCTTG
1690012 TCAAAATACT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.11
20 12 0.26
21 29 0.63
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (21 bp):
AAACTTCTTGAGAAAGTTTCA
Found at i:1690012 original size:21 final size:20
Alignment explanation
Indices: 1689955--1690017 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 20
1689945 GTCTTGGAAG
1689955 GTTTCAAAACTCTTGTAGAAA
1 GTTTCAAAACTCTTGTA-AAA
1689976 GTTTCAAAACTCTTGTAAAA
1 GTTTCAAAACTCTTGTAAAA
*
1689996 GTTTCGAAACTTCTTGTCAAAA
1 GTTTCAAAAC-TCTTGT-AAAA
1690018 TACTCATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
20 12 0.31
21 23 0.59
22 4 0.10
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (20 bp):
GTTTCAAAACTCTTGTAAAA
Found at i:1693418 original size:35 final size:34
Alignment explanation
Indices: 1693372--1693482 Score: 123
Period size: 35 Copynumber: 3.2 Consensus size: 34
1693362 AAAATAGTCC
*
1693372 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAA-TAAT
* * *
1693407 TCAATTTCATTCTAAACCCTAAATTCCAAAAAAA
1 TCAATTTCATTCTAAACCCCAAATTCCAAATAAT
** * * *
1693441 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTC-CAAATAAT
1693476 TCAATTT
1 TCAATTT
1693483 AAGGTTTAGA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
34 24 0.39
35 38 0.61
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAATAAT
Found at i:1696349 original size:22 final size:22
Alignment explanation
Indices: 1696309--1696350 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1696299 CAATAATTTT
*
1696309 TAATTATTGACTTTCAAATTAG
1 TAATTATTGACTGTCAAATTAG
1696331 TAATTATTGACATGT-AAATT
1 TAATTATTGAC-TGTCAAATT
1696351 TTAGCAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (22 bp):
TAATTATTGACTGTCAAATTAG
Found at i:1702454 original size:10 final size:10
Alignment explanation
Indices: 1702439--1702520 Score: 110
Period size: 10 Copynumber: 8.2 Consensus size: 10
1702429 CTTTTCTGTT
*
1702439 TATATACATA
1 TATATATATA
*
1702449 TATATACATA
1 TATATATATA
*
1702459 CATATATATA
1 TATATATATA
* * *
1702469 CATACATACA
1 TATATATATA
1702479 TATATATATA
1 TATATATATA
1702489 TATATATATA
1 TATATATATA
1702499 TATATATATA
1 TATATATATA
1702509 TATATATATA
1 TATATATATA
1702519 TA
1 TA
1702521 ATTTGAAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 65 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATATATA
Found at i:1702459 original size:14 final size:14
Alignment explanation
Indices: 1702439--1702520 Score: 110
Period size: 14 Copynumber: 5.9 Consensus size: 14
1702429 CTTTTCTGTT
1702439 TATATACATATATA
1 TATATACATATATA
*
1702453 TACATACATATATA
1 TATATACATATATA
* *
1702467 TACATACATACATA
1 TATATACATATATA
*
1702481 TATATATATATATA
1 TATATACATATATA
*
1702495 TATATATATATATA
1 TATATACATATATA
*
1702509 TATATATATATA
1 TATATACATATA
1702521 ATTTGAAACA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 63 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TATATACATATATA
Found at i:1702473 original size:18 final size:18
Alignment explanation
Indices: 1702446--1702520 Score: 105
Period size: 18 Copynumber: 4.2 Consensus size: 18
1702436 GTTTATATAC
1702446 ATATATATACATACATAT
1 ATATATATACATACATAT
*
1702464 ATATACATACATACATAT
1 ATATATATACATACATAT
* *
1702482 ATATATATATATATATAT
1 ATATATATACATACATAT
* *
1702500 ATATATATATATATATAT
1 ATATATATACATACATAT
1702518 ATA
1 ATA
1702521 ATTTGAAACA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATATATACATACATAT
Found at i:1702485 original size:4 final size:4
Alignment explanation
Indices: 1702439--1702520 Score: 110
Period size: 4 Copynumber: 20.5 Consensus size: 4
1702429 CTTTTCTGTT
* * * * * *
1702439 TATA TACA TATA TATA CATA CATA TATA TACA TACA TACA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
1702487 TATA TATA TATA TATA TATA TATA TATA TATA TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TA
1702521 ATTTGAAACA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 72 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (4 bp):
TATA
Found at i:1708049 original size:59 final size:61
Alignment explanation
Indices: 1707986--1708113 Score: 145
Period size: 59 Copynumber: 2.1 Consensus size: 61
1707976 GTACATATAA
* * * * *
1707986 ATAGTTGAGTAACCATTTTATAATTTTTAATAATTGAAT-GACTCAACAA-AATAATA-CCT
1 ATAGTCGAGGAACAATTTTATAACTTTTAATAATTG-ATCGACTCAAAAATAATAATATCCT
* * *
1708045 ATAGTCGAGGGACAATTTTATAACTTTTAATAGTTGATCGATTCAAAAATAATAATATCCT
1 ATAGTCGAGGAACAATTTTATAACTTTTAATAATTGATCGACTCAAAAATAATAATATCCT
*
1708106 ATAATCGA
1 ATAGTCGA
1708114 AGATCATTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
58 2 0.04
59 38 0.67
60 7 0.12
61 10 0.18
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (61 bp):
ATAGTCGAGGAACAATTTTATAACTTTTAATAATTGATCGACTCAAAAATAATAATATCCT
Found at i:1710937 original size:31 final size:31
Alignment explanation
Indices: 1710868--1710937 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
1710858 TACTCGTGGC
* *
1710868 GACCACATCTTAATTAAATAAAAACAAAAGT
1 GACCATATCTTAATTAAACAAAAACAAAAGT
* * * *
1710899 AATCATATCTTAATTAAACATAAATAAAAGT
1 GACCATATCTTAATTAAACAAAAACAAAAGT
1710930 GACCATAT
1 GACCATAT
1710938 ATTATGTTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.27
Consensus pattern (31 bp):
GACCATATCTTAATTAAACAAAAACAAAAGT
Found at i:1713958 original size:31 final size:30
Alignment explanation
Indices: 1713871--1713958 Score: 97
Period size: 32 Copynumber: 2.9 Consensus size: 30
1713861 AGTTTAAGAA
*
1713871 ATTATAAAATAATAATTAAACTTA-TAAAT
1 ATTATAAAATGATAATTAAACTTATTAAAT
* *
1713900 AGTTACAAAATGATAATAAAATCTTATTAAACT
1 A-TTATAAAATGATAATTAAA-CTTATTAAA-T
* *
1713933 ATTATAAAATGGTCATTAAACTTATT
1 ATTATAAAATGATAATTAAACTTATT
1713959 GCATTGTTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 1 0.02
30 16 0.33
31 10 0.21
32 19 0.40
33 2 0.04
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.38
Consensus pattern (30 bp):
ATTATAAAATGATAATTAAACTTATTAAAT
Found at i:1720713 original size:3 final size:3
Alignment explanation
Indices: 1720705--1720729 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1720695 CCCAATCTTT
1720705 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1720730 ATATATATAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1720734 original size:2 final size:2
Alignment explanation
Indices: 1720727--1720759 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1720717 TTATTATTAT
1720727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1720760 GAATTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1720923 original size:18 final size:18
Alignment explanation
Indices: 1720900--1720935 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1720890 GAAGAAACCG
1720900 TATCATATTTCTATACTT
1 TATCATATTTCTATACTT
1720918 TATCATATTTCTATACTT
1 TATCATATTTCTATACTT
1720936 AGAGATATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.56
Consensus pattern (18 bp):
TATCATATTTCTATACTT
Found at i:1720967 original size:2 final size:2
Alignment explanation
Indices: 1720960--1720985 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1720950 ATGTATAAAC
1720960 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
1720986 CATTGATAAT
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:1721193 original size:2 final size:2
Alignment explanation
Indices: 1721186--1721214 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1721176 TGGAAGGATG
1721186 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
1721215 CATTCACCAG
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:1727883 original size:22 final size:22
Alignment explanation
Indices: 1727792--1727872 Score: 144
Period size: 22 Copynumber: 3.7 Consensus size: 22
1727782 AAATCGAATA
*
1727792 TATATATATATATGTACGCATG
1 TATATGTATATATGTACGCATG
1727814 TATATGTATATATGTACGCATG
1 TATATGTATATATGTACGCATG
*
1727836 TATATGTCTATATGTACGCATG
1 TATATGTATATATGTACGCATG
1727858 TATATGTATATATGT
1 TATATGTATATATGT
1727873 GTGTGTGTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (22 bp):
TATATGTATATATGTACGCATG
Found at i:1736847 original size:3 final size:3
Alignment explanation
Indices: 1736839--1736863 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1736829 ATTATACCAT
1736839 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
1736864 AACCCTATTT
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:1737659 original size:22 final size:23
Alignment explanation
Indices: 1737634--1737677 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
1737624 AAGAAATATT
* *
1737634 ATCTTATTCAATAAA-AATATAA
1 ATCTAATTCAAAAAATAATATAA
*
1737656 ATCTAATTGAAAAAATAATATA
1 ATCTAATTCAAAAAATAATATA
1737678 TAAAGAGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (23 bp):
ATCTAATTCAAAAAATAATATAA
Found at i:1740179 original size:31 final size:31
Alignment explanation
Indices: 1740103--1740193 Score: 92
Period size: 32 Copynumber: 2.9 Consensus size: 31
1740093 TTGTAACCGC
* * *
1740103 TCGATTAGTTTTAATGACAATTTTGTACTAGT
1 TCGATAAG-TTTAATGACAATTTTGTAATAAT
* * *
1740135 TTGATAAAGTTTAATGATAATTTTTTAATAAT
1 TCGAT-AAGTTTAATGACAATTTTGTAATAAT
* *
1740167 TCGATAAGTTTAACGACTATTTTGTAA
1 TCGATAAGTTTAATGACAATTTTGTAA
1740194 CTTCCGAAAC
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
31 18 0.38
32 27 0.57
33 2 0.04
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (31 bp):
TCGATAAGTTTAATGACAATTTTGTAATAAT
Found at i:1741145 original size:25 final size:26
Alignment explanation
Indices: 1741091--1741151 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
1741081 TCCATGCCCC
*
1741091 AATATATATATATATATAATTTAAAT
1 AATATATATATATAAATAATTTAAAT
*
1741117 AATATAT-TATATAAATTATGTTAAA-
1 AATATATATATATAAATAAT-TTAAAT
1741142 AATAT-TATAT
1 AATATATATAT
1741152 TAGTCTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 1 0.03
25 18 0.58
26 12 0.39
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AATATATATATATAAATAATTTAAAT
Found at i:1742609 original size:60 final size:60
Alignment explanation
Indices: 1742497--1742609 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
1742487 ATAGTCAAGT
* * *
1742497 GACTATTTTGTAACTTTTAATAGTCGAAGAACTCAACAAAGCAATACTCTATAATTGGAG
1 GACTATTTTGTAACTTCTAATAGTAGAAGAACTCAACAAAGCAATACCCTATAATTGGAG
* * * *
1742557 GACTATTTTGTAACTTCTAATAGTAG-AGAGACTTAATAAAGTATTACCCTATA
1 GACTATTTTGTAACTTCTAATAGTAGAAGA-ACTCAACAAAGCAATACCCTATA
1742610 TCCGAGACCA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 3 0.07
60 42 0.93
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (60 bp):
GACTATTTTGTAACTTCTAATAGTAGAAGAACTCAACAAAGCAATACCCTATAATTGGAG
Found at i:1746842 original size:20 final size:20
Alignment explanation
Indices: 1746799--1746851 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1746789 CAATGAATCG
* * *
1746799 GCTGAGAACCGGTAGAACCG
1 GCTGAGAATCGGTAGAAACA
1746819 GCTGAGAATCGGTAGAAACA
1 GCTGAGAATCGGTAGAAACA
*
1746839 GCTGAAAATCGGT
1 GCTGAGAATCGGT
1746852 GTGAACCGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.19, G:0.32, T:0.15
Consensus pattern (20 bp):
GCTGAGAATCGGTAGAAACA
Found at i:1747311 original size:70 final size:70
Alignment explanation
Indices: 1747193--1747325 Score: 203
Period size: 70 Copynumber: 1.9 Consensus size: 70
1747183 TAGAAGTCAG
* ** * * *
1747193 TTGGGATGCTCTTCTATGTTTTTTAGTCATGTGTGATTGTTTTTTTCTCCTATTTTTACTCTTTA
1 TTGGGATGCTCTTCTATGTTTCTTAACCATATGAGATTGTTTTGTTCTCCTATTTTTACTCTTTA
1747258 GATTT
66 GATTT
*
1747263 TTGGGATGCTCTTCTATGTTTCTTAACCATATGAGATTGTTTTGTTCTCCTATTTTTGCTCTT
1 TTGGGATGCTCTTCTATGTTTCTTAACCATATGAGATTGTTTTGTTCTCCTATTTTTACTCTT
1747326 CTATGCTCTT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 56 1.00
ACGTcount: A:0.14, C:0.15, G:0.16, T:0.56
Consensus pattern (70 bp):
TTGGGATGCTCTTCTATGTTTCTTAACCATATGAGATTGTTTTGTTCTCCTATTTTTACTCTTTA
GATTT
Found at i:1751922 original size:30 final size:30
Alignment explanation
Indices: 1751886--1751988 Score: 154
Period size: 30 Copynumber: 3.4 Consensus size: 30
1751876 CATTTACTGT
1751886 TCAGACGGCTTCTCGACATGTTCAGCCACC
1 TCAGACGGCTTCTCGACATGTTCAGCCACC
*
1751916 TCAGACGGCTTCTTGACATGTTCAGCCACC
1 TCAGACGGCTTCTCGACATGTTCAGCCACC
* *
1751946 TCGGACGGCTTCTCAACCA-GTTCAGCCACC
1 TCAGACGGCTTCTCGA-CATGTTCAGCCACC
*
1751976 TCGGACGGCTTCT
1 TCAGACGGCTTCT
1751989 TAACCTCCCG
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 66 0.97
31 2 0.03
ACGTcount: A:0.18, C:0.36, G:0.21, T:0.24
Consensus pattern (30 bp):
TCAGACGGCTTCTCGACATGTTCAGCCACC
Found at i:1758821 original size:2 final size:2
Alignment explanation
Indices: 1758805--1758848 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
1758795 AAAAATATTT
1758805 TA TA -A TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1758847 TA
1 TA
1758849 ATTTTGGCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1763546 original size:24 final size:24
Alignment explanation
Indices: 1763492--1763547 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
1763482 AATATGCAAT
* * *
1763492 AAAAGAAAAAAAGAAAAAATGTTA
1 AAAAAAAAAAAAGAAAAAATATAA
*
1763516 AACAAAAAAAAAGAAAAAA-ATAA
1 AAAAAAAAAAAAGAAAAAATATAA
*
1763539 GAAAAAAAA
1 AAAAAAAAA
1763548 CATATAGAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.82, C:0.02, G:0.09, T:0.07
Consensus pattern (24 bp):
AAAAAAAAAAAAGAAAAAATATAA
Found at i:1771645 original size:20 final size:20
Alignment explanation
Indices: 1771620--1771712 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
1771610 TTTTCCCAAT
1771620 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1771640 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1771660 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
1771681 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1771702 TCGCAATGCGA
1 TCGCAATGCGA
1771713 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1771662 original size:41 final size:41
Alignment explanation
Indices: 1771617--1771712 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
1771607 CGATTTTCCC
1771617 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1771658 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1771699 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1771713 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:1771666 original size:21 final size:20
Alignment explanation
Indices: 1771620--1771712 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1771610 TTTTCCCAAT
*
1771620 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1771640 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1771660 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
1771681 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1771702 TCGCAATGCGA
1 TCGCAATGCGA
1771713 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1771725 original size:41 final size:41
Alignment explanation
Indices: 1771639--1771773 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
1771629 GAATAAGTAA
* * *
1771639 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
1771680 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
1771721 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1771762 TTCGCAACGCGA
1 ATCGCAACGCGA
1771774 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1771726 original size:20 final size:20
Alignment explanation
Indices: 1771701--1771795 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1771691 AATTGGGAAA
*
1771701 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1771721 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1771742 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1771762 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1771782 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1771796 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1772011 original size:22 final size:22
Alignment explanation
Indices: 1771983--1772026 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1771973 CACTCTCTCA
1771983 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1772005 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1772027 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1772315 original size:20 final size:20
Alignment explanation
Indices: 1772290--1772327 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1772280 CGATTCTCTC
1772290 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1772310 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1772328 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1773668 original size:18 final size:18
Alignment explanation
Indices: 1773647--1773691 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1773637 TCCACTTCGG
*
1773647 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
1773665 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
1773683 GAGCCATCA
1 GAGCCATCA
1773692 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1774189 original size:20 final size:20
Alignment explanation
Indices: 1774164--1774209 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1774154 TAGTTTACTT
1774164 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
1774184 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1774204 TCGCAA
1 TCGCAA
1774210 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1774218 original size:19 final size:20
Alignment explanation
Indices: 1774175--1774219 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1774165 CGCAACACGA
1774175 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
1774195 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
1774214 AAATGA
1 AAATGA
1774220 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:1774225 original size:19 final size:19
Alignment explanation
Indices: 1774183--1774298 Score: 74
Period size: 19 Copynumber: 6.6 Consensus size: 19
1774173 GAAAATGACT
***
1774183 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
1774203 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1774222 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
1774236 ATCGCAACGCAAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1774254 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1774268 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1774287 ATCGCAATGCGA
1 ATCGCAATGCGA
1774299 TTTGTGTTTC
Statistics
Matches: 75, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
14 20 0.27
15 1 0.01
16 4 0.05
17 2 0.03
18 11 0.15
19 27 0.36
20 10 0.13
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1774238 original size:14 final size:14
Alignment explanation
Indices: 1774219--1774276 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1774209 ATGCGAAATG
1774219 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1774233 AAAATCGCAACGCAAA
1 AAAATCGCAACG--AC
1774249 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1774265 AAAATCGCAACG
1 AAAATCGCAACG
1774277 CGAAATGAAA
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:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1774261 original size:32 final size:33
Alignment explanation
Indices: 1774203--1774293 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1774193 GGAAATGGCT
*
1774203 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
1774236 ATCGCAACGCAAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1774268 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
1774294 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1774329 original size:14 final size:14
Alignment explanation
Indices: 1774310--1774399 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
1774300 TTGTGTTTCG
1774310 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1774324 CGTTGCGATTTCATTTT
1 CGTTGCGA-TT--TTGT
1774341 GCGTTGCGATTTTGT
1 -CGTTGCGATTTTGT
*
1774356 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1774372 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1774388 CGTTGCGATTTT
1 CGTTGCGATTTT
1774400 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 31 0.48
15 5 0.08
16 4 0.06
17 5 0.08
18 19 0.30
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1774348 original size:32 final size:32
Alignment explanation
Indices: 1774305--1774415 Score: 195
Period size: 32 Copynumber: 3.4 Consensus size: 32
1774295 GCGATTTGTG
1774305 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
*
1774337 TTTTGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1774369 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
*
1774402 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1774416 AGCCATTTCC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 57 0.76
33 18 0.24
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:1774414 original size:19 final size:19
Alignment explanation
Indices: 1774324--1774473 Score: 99
Period size: 20 Copynumber: 8.4 Consensus size: 19
1774314 GCGATTTTGT
*
1774324 CGTTGCGA-TTTCATTTTG
1 CGTTGCGATTTTCATTTCG
*
1774342 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1774356 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1774374 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1774388 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1774407 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
1774427 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1774446 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1774466 TGTTGCGA
1 CGTTGCGA
1774474 AAGTAAACTA
Statistics
Matches: 107, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
14 19 0.18
15 3 0.03
16 6 0.06
17 2 0.02
18 22 0.21
19 26 0.24
20 29 0.27
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1776342 original size:14 final size:14
Alignment explanation
Indices: 1776323--1776358 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1776313 ATTGTTTAAT
1776323 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1776337 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1776351 TGATTTGT
1 TGATTTGT
1776359 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1777659 original size:24 final size:24
Alignment explanation
Indices: 1777603--1777661 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
1777593 AGTCAGTATT
* *
1777603 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
1777627 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
1777651 CGAATTTTGAT
1 CGAAATTTGAT
1777662 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:1777853 original size:12 final size:12
Alignment explanation
Indices: 1777836--1777860 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1777826 ATATAATCCT
1777836 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1777848 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1777860 G
1 G
1777861 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1780595 original size:20 final size:19
Alignment explanation
Indices: 1780550--1780690 Score: 86
Period size: 19 Copynumber: 7.8 Consensus size: 19
1780540 TCTTTTGGTT
1780550 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
1780569 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
1780590 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
1780609 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
1780623 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
1780642 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
1780656 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
1780675 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1780691 TGCGATTTTG
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 18 0.19
16 4 0.04
17 4 0.04
19 39 0.42
20 26 0.28
21 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1780632 original size:33 final size:33
Alignment explanation
Indices: 1780575--1780673 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
1780565 ACGAGATAAT
* *
1780575 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
1780609 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
1780642 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
1780674 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:1780667 original size:19 final size:19
Alignment explanation
Indices: 1780645--1780695 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1780635 GCGACGAGAG
1780645 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1780664 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1780683 AATCGCAATGCGA
1 AATCGCAACGCGA
1780696 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1781355 original size:20 final size:20
Alignment explanation
Indices: 1781262--1781355 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1781252 CGCTAAATAA
*
1781262 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
1781282 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
1781302 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
1781323 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1781343 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1781356 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1781374 original size:41 final size:41
Alignment explanation
Indices: 1781283--1781417 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
1781273 AAAGTCAGTA
* * * ** *
1781283 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
1781323 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
1781365 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1781406 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1781418 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1781388 original size:20 final size:20
Alignment explanation
Indices: 1781344--1781436 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1781334 ATAGTCAGTA
* **
1781344 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
1781365 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
1781385 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
1781406 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
1781426 TCGCATTGCGA
1 TCGCATTGCGA
1781437 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:1781418 original size:41 final size:41
Alignment explanation
Indices: 1781344--1781439 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
1781334 ATAGTCAGTA
*
1781344 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1781385 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1781426 TCGCATTGCGAATT
1 TCGCATTGCGAATT
1781440 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1785810 original size:21 final size:21
Alignment explanation
Indices: 1785784--1785840 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
1785774 ACAGTACTGA
1785784 CGTGACAGTTCACAACGTTGG
1 CGTGACAGTTCACAACGTTGG
1785805 CGTGACAGTTCACAACGTTGG
1 CGTGACAGTTCACAACGTTGG
1785826 CGTGACAGTTCACAA
1 CGTGACAGTTCACAA
1785841 TGCTGACGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (21 bp):
CGTGACAGTTCACAACGTTGG
Found at i:1785850 original size:21 final size:21
Alignment explanation
Indices: 1785780--1785853 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
1785770 TGTTACAGTA
1785780 CTGACGTGACAGTTCACAACG
1 CTGACGTGACAGTTCACAACG
* *
1785801 TTGGCGTGACAGTTCACAACG
1 CTGACGTGACAGTTCACAACG
* * *
1785822 TTGGCGTGACAGTTCACAATG
1 CTGACGTGACAGTTCACAACG
1785843 CTGACGTGACA
1 CTGACGTGACA
1785854 ATCCAATGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (21 bp):
CTGACGTGACAGTTCACAACG
Found at i:1787239 original size:31 final size:29
Alignment explanation
Indices: 1787181--1787239 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
1787171 TGACCACGCT
* * *
1787181 TTAATTAAATAAACGGAAGTGATCATATC
1 TTAATTAAATAAACGAAAATGACCATATC
1787210 TTAATTAAATAAAAACGAAAATGACCATAT
1 TTAATTAAAT--AAACGAAAATGACCATAT
1787240 ATTATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
31 15 0.60
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (29 bp):
TTAATTAAATAAACGAAAATGACCATATC
Found at i:1794262 original size:21 final size:22
Alignment explanation
Indices: 1794220--1794262 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1794210 TTCGTCACAT
**
1794220 TATCAATCACCGTAGATTGTCA
1 TATCAATCACCGTAGACCGTCA
*
1794242 TATCAA-CACCGTGGACCGTCA
1 TATCAATCACCGTAGACCGTCA
1794263 CGTCAGTACC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (22 bp):
TATCAATCACCGTAGACCGTCA
Found at i:1797250 original size:24 final size:26
Alignment explanation
Indices: 1797219--1797269 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 26
1797209 TATTAATAAA
*
1797219 TTTTAATATTTAA-A-ATTATTTATT
1 TTTTAATATTTAATATATTAGTTATT
1797243 TTTTAATATTTAATATATTAGTTATT
1 TTTTAATATTTAATATATTAGTTATT
1797269 T
1 T
1797270 ATAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 13 0.54
25 1 0.04
26 10 0.42
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTAATATTTAATATATTAGTTATT
Found at i:1804895 original size:23 final size:22
Alignment explanation
Indices: 1804853--1804910 Score: 89
Period size: 23 Copynumber: 2.6 Consensus size: 22
1804843 ATAGGGCAGA
* *
1804853 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
1804875 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
1804898 GGGAACCGATTCC
1 GGGAACCGATTCC
1804911 TCATAGGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.24, C:0.29, G:0.28, T:0.19
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:1806906 original size:17 final size:17
Alignment explanation
Indices: 1806881--1806919 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1806871 ATTTTGAATT
*
1806881 TTTTTTGGAATGTTTGA
1 TTTTGTGGAATGTTTGA
*
1806898 TTTTGTGGATTGTTTGA
1 TTTTGTGGAATGTTTGA
*
1806915 CTTTG
1 TTTTG
1806920 AATTTGTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.03, G:0.26, T:0.59
Consensus pattern (17 bp):
TTTTGTGGAATGTTTGA
Found at i:1808317 original size:12 final size:12
Alignment explanation
Indices: 1808300--1808335 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1808290 TTATTTTTAC
1808300 TATAACTATTAT
1 TATAACTATTAT
1808312 TATAACTATT-T
1 TATAACTATTAT
1808323 T-TAA-TATTAT
1 TATAACTATTAT
1808333 TAT
1 TAT
1808336 TTCCTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
9 4 0.18
10 5 0.23
11 3 0.14
12 10 0.45
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (12 bp):
TATAACTATTAT
Found at i:1808430 original size:2 final size:2
Alignment explanation
Indices: 1808425--1808450 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1808415 TTTTGACATA
1808425 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
1808451 TTCACCTATT
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:1810316 original size:15 final size:15
Alignment explanation
Indices: 1810296--1810371 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
1810286 AAAGAAATCC
1810296 TAATATTTTATAATA
1 TAATATTTTATAATA
*
1810311 TAATATTTGATAATA
1 TAATATTTTATAATA
* *
1810326 TTTTATATATTA-AATAA
1 --TAATATTTTATAAT-A
1810343 TAA-A-TTTATAATA
1 TAATATTTTATAATA
*
1810356 TAATATTTGATAATA
1 TAATATTTTATAATA
1810371 T
1 T
1810372 TTTATATATT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
13 7 0.15
14 5 0.10
15 25 0.52
16 3 0.06
17 8 0.17
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TAATATTTTATAATA
Found at i:1810342 original size:19 final size:19
Alignment explanation
Indices: 1810320--1810387 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 19
1810310 ATAATATTTG
1810320 ATAATATTTTATATATTAA
1 ATAATATTTTATATATTAA
**
1810339 ATAATAAATTTATAATATAATATTTG
1 ATAAT--A-TT-T--TAT-ATATTAA
1810365 ATAATATTTTATATATTAA
1 ATAATATTTTATATATTAA
1810384 ATAA
1 ATAA
1810388 CTTCTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 14 0.37
20 3 0.08
21 1 0.03
22 3 0.08
23 3 0.08
24 1 0.03
25 3 0.08
26 10 0.26
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (19 bp):
ATAATATTTTATATATTAA
Found at i:1810351 original size:45 final size:45
Alignment explanation
Indices: 1810302--1810387 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
1810292 ATCCTAATAT
1810302 TTTATAATATAATATTTGATAATATTTTATATATTAAATAATAAA
1 TTTATAATATAATATTTGATAATATTTTATATATTAAATAATAAA
1810347 TTTATAATATAATATTTGATAATATTTTATATATTAAATAA
1 TTTATAATATAATATTTGATAATATTTTATATATTAAATAA
1810388 CTTCTATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (45 bp):
TTTATAATATAATATTTGATAATATTTTATATATTAAATAATAAA
Found at i:1812622 original size:41 final size:41
Alignment explanation
Indices: 1812584--1813074 Score: 536
Period size: 41 Copynumber: 11.9 Consensus size: 41
1812574 TGTTTTTTCA
* * *
1812584 ACAAACGCCGCAAAAGAGTAGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* *
1812625 ACAAACGCCGCTAAAGACTCGTAATTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * *
1812666 ACAAACGCCGCTATAGAATTGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * * *
1812707 ACAAACGCCGTTATACACAT-GTACTATAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGAC-TCGTACTTTAGTGGCGTTTTTAT
* * * * * * *
1812748 AAAAACGTCGTTATACACAT-GTACTATAGTGGTGTTTTTAT
1 ACAAACGCCGCTAAAGAC-TCGTACTTTAGTGGCGTTTTTAT
* * *
1812789 AAAAACGCCGCTAAAGACTCATACTTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * * *
1812830 ACAAACTCCGCTAAAGACGCGTACTTTAGTGACATTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * * * * * *
1812871 GCAAACGCCGTTATACACTTGTACTATAGTGGCGTTTGTGTTT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTT-T-TAT
* * *
1812914 ACAAACGTCGCTAAAGACTCGTAATTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * *
1812955 ACAAACGCCGCTAAAGACTCGTACTTTATTGACATTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
1812996 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * * * *
1813037 TCAAACGCCGCTATACACTTGTACTATAGTGGCGTTTT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTT
1813075 ATAGCGGCGT
Statistics
Matches: 383, Mismatches: 63, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
40 1 0.00
41 349 0.91
42 3 0.01
43 30 0.08
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
Found at i:1815378 original size:43 final size:42
Alignment explanation
Indices: 1815328--1815650 Score: 326
Period size: 43 Copynumber: 7.5 Consensus size: 42
1815318 AAGGTAATTA
* * *
1815328 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACTTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTAACCTTTT
* * * *
1815371 GTGGCGTTTGTGTTCAAAAACGTCGTTATAGGTCTAACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTAACCTTTT
* * *
1815414 GTGGCGTTTGTGTCCAAAAACGTCGCTATAGGTTTAACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTAACCTTTT
* *
1815457 GCGGCGTTTGTTCTAAAAACGCCAG-TATAGGTCT-TCTCTTTT
1 GCGGCGTTTGTTCCAAAAACGCC-GCTATAGGTCTAAC-CTTTT
* *
1815499 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTAACCTTTT
* * * * ** *
1815542 GCGACGTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGGTC-TAACCTTTT
* * * *
1815585 GCGGCGTTTATTCCAAAAACGCCGCTATAGATATCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGGTCT-AACCTTTT
*
1815628 GCGGCGTTTGTTCAAAAAACGCC
1 GCGGCGTTTGTTCCAAAAACGCC
1815651 ATAATAGATA
Statistics
Matches: 237, Mismatches: 36, Indels: 14
0.83 0.13 0.05
Matches are distributed among these distances:
41 1 0.00
42 55 0.23
43 180 0.76
44 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGGTCTAACCTTTT
Found at i:1815499 original size:128 final size:128
Alignment explanation
Indices: 1815328--1815650 Score: 348
Period size: 128 Copynumber: 2.5 Consensus size: 128
1815318 AAGGTAATTA
* * *
1815328 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACTTTTTGTGGCGTTTGTGTTCAAAAACG
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTATCCAAAAACG
* * * * * * * *
1815393 TCGTTATAGGTCTAACCTTTTGTGGCGTTTGTGTCCAAAAACGTCGCTATAGGT-TTAACCTTTT
65 CCGCTATAGATCTAACCTTTTGCGACGTTT-TGTCCAAAAACGCCGCTATAGATCATAACCTTTT
* *
1815457 GCGGCGTTTGTTCTAAAAACGCCAG-TATAGGTCT-TCTCTTTTGCGGCGTTTGTATCCAAAAAC
1 GCGGCGTTTGTTCAAAAAACGCC-GCTATAGGTCTGACT-TTTTGCGGCGTTTGTATCCAAAAAC
* * * * * *
1815520 GCCGCTATAGATCTGACCTTTTGCGACGTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTT
64 GCCGCTATAGATCTAACCTTTTGCGACGTTTTGTCCAAAAACGCCGCTATAGATCATAACCTTTT
* * * * * *
1815585 GCGGCGTTTATTCCAAAAACGCCGCTATAGATATCGACCTTTTGCGGCGTTTGT-TCAAAAAACG
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGGTCT-GACTTTTTGCGGCGTTTGTATCCAAAAACG
1815649 CC
65 CC
1815651 ATAATAGATA
Statistics
Matches: 162, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
127 20 0.12
128 114 0.70
129 27 0.17
130 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (128 bp):
GCGGCGTTTGTTCAAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTATCCAAAAACGC
CGCTATAGATCTAACCTTTTGCGACGTTTTGTCCAAAAACGCCGCTATAGATCATAACCTTTT
Found at i:1815515 original size:85 final size:86
Alignment explanation
Indices: 1815328--1815650 Score: 370
Period size: 85 Copynumber: 3.8 Consensus size: 86
1815318 AAGGTAATTA
* * * *
1815328 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACTTTTTGTGGCGTTTGTGT-TCAAAAAC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCT-AAAAAC
* *
1815392 GTCGTTATAGGTCTAAC-CTTTT
64 GCCGCTATAGGTCTAACTCTTTT
* * * * * *
1815414 GTGGCGTTTGTGTCCAAAAACGTCGCTATAGGTTTAACCTTTTGCGGCGTTTGTTCTAAAAACGC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
*
1815479 CAG-TATAGGTCT-TCTCTTTT
66 C-GCTATAGGTCTAACTCTTTT
* * *
1815499 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGACGTTTTTTCTAGAAACGC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
**
1815564 CGCTATATATCATAACT-TTTT
66 CGCTATAGGTC-TAACTCTTTT
* * *
1815585 GCGGCGTTTAT-TCCAAAAACGCCGCTATAGATATCGACCTTTTGCGGCGTTTGTTCAAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCTAAAAACG
1815649 CC
65 CC
1815651 ATAATAGATA
Statistics
Matches: 202, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
84 2 0.01
85 108 0.53
86 90 0.45
87 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (86 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
CGCTATAGGTCTAACTCTTTT
Found at i:1818512 original size:32 final size:32
Alignment explanation
Indices: 1818471--1818565 Score: 136
Period size: 32 Copynumber: 3.0 Consensus size: 32
1818461 GCTTGATTCG
1818471 GATTGACTCGATTCGAACTCGAGCTGGACTCA
1 GATTGACTCGATTCGAACTCGAGCTGGACTCA
* *
1818503 GATTGACTCGATTCGAACTCGAGTTGGACTTA
1 GATTGACTCGATTCGAACTCGAGCTGGACTCA
* * * *
1818535 GATCGACTCGATTCAAACTCGGGCTCGACTC
1 GATTGACTCGATTCGAACTCGAGCTGGACTC
1818566 GAAACCTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.26
Consensus pattern (32 bp):
GATTGACTCGATTCGAACTCGAGCTGGACTCA
Found at i:1821379 original size:14 final size:14
Alignment explanation
Indices: 1821336--1821370 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1821326 CGATTTATTG
*
1821336 ATCGACTAATTCAA
1 ATCGAATAATTCAA
1821350 ATCGAATAATTCAA
1 ATCGAATAATTCAA
1821364 ATCGAAT
1 ATCGAAT
1821371 GTTGCAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (14 bp):
ATCGAATAATTCAA
Found at i:1825885 original size:29 final size:29
Alignment explanation
Indices: 1825841--1825909 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
1825831 TAAATTTGTT
* * * * *
1825841 TTCGTCCCCTAGAATTTTCCAAGTTTAAA
1 TTCGTCTCCTAAAATTTTACAAATTCAAA
*
1825870 TTCGTCTCCTAAAATTTTATAAATTCAAA
1 TTCGTCTCCTAAAATTTTACAAATTCAAA
1825899 TTCG-CTCCTAA
1 TTCGTCTCCTAA
1825910 TATAAAATCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 7 0.21
29 27 0.79
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.39
Consensus pattern (29 bp):
TTCGTCTCCTAAAATTTTACAAATTCAAA
Found at i:1826764 original size:2 final size:2
Alignment explanation
Indices: 1826757--1826783 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1826747 TATGTTGTTA
1826757 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1826784 CACGTTCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1826948 original size:2 final size:2
Alignment explanation
Indices: 1826941--1826967 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1826931 TTCATTCATT
1826941 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1826968 GTTAATGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1838897 original size:21 final size:21
Alignment explanation
Indices: 1838868--1838911 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1838858 TGGTCACTCG
* * *
1838868 AACGTTGATTGTTAGTCACTT
1 AACGATGATGGTTAATCACTT
1838889 AACGATGATGGTTAATCACTT
1 AACGATGATGGTTAATCACTT
1838910 AA
1 AA
1838912 GAATTTTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (21 bp):
AACGATGATGGTTAATCACTT
Found at i:1839320 original size:21 final size:21
Alignment explanation
Indices: 1839282--1839321 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1839272 ACTCTATACT
*
1839282 TTTAAAACTTTTTATTTAAAA
1 TTTAAAACATTTTATTTAAAA
1839303 TTTAAAATCATTTT-TTTAA
1 TTTAAAA-CATTTTATTTAA
1839322 CAAAATACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAAAACATTTTATTTAAAA
Found at i:1844361 original size:141 final size:141
Alignment explanation
Indices: 1844183--1844568 Score: 539
Period size: 141 Copynumber: 2.7 Consensus size: 141
1844173 CAAGAGTAAC
* *
1844183 GATTCCGGACAACA-CATTGAAAGAAGAAAAGTAAAAAAATCAACTTCAAGACTATATTCAAATA
1 GATTCCCGACAACATCATCGAAAGAAGAAAAG-AAAAAAATCAACTTCAAGACTATATTCAAATA
*
1844247 TGTGCATTCAAGTGGGATTCGAAACATAATCAATCAACAAAATGCAATATACCTCAAGATGA-TG
65 TGTGCATTCAAGTGGGATTCGAAACATAATCAATCAACAAAATGCAATATACCCCAAGATGAGT-
1844311 GGTAACAATAT-A
129 GGTAACAATATGA
* *
1844323 TGATTCCCGACAACATCATCGAAAGAAGAAAAGGAAAAAATCAACTTCAAGACTATATTCAATTA
1 -GATTCCCGACAACATCATCGAAAGAAGAAAAGAAAAAAATCAACTTCAAGACTATATTCAAATA
* *
1844388 TGTGCATTCAAGTGGGATTTGAAACATAATCAATCAACCAAATGCAATATACCCCAAGATGAGTG
65 TGTGCATTCAAGTGGGATTCGAAACATAATCAATCAACAAAATGCAATATACCCCAAGATGAGTG
* *
1844453 GTAACGATGTGA
130 GTAACAATATGA
* * * * * *
1844465 GATTCCCAACAACATCATCGAAAG-A-AAAAGTAAAATATCAACTTCAAGGCTACATTCAAATAA
1 GATTCCCGACAACATCATCGAAAGAAGAAAAGAAAAAAATCAACTTCAAGACTATATTCAAATAT
* * *
1844528 ATGCATTCAAGAGGGATTCGAATCATAATCAATCAAGCAAA
66 GTGCATTCAAGTGGGATTCGAAACATAATCAATCAA-CAAA
1844569 TGGCAAATGC
Statistics
Matches: 220, Mismatches: 21, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
139 64 0.29
140 4 0.02
141 134 0.61
142 18 0.08
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (141 bp):
GATTCCCGACAACATCATCGAAAGAAGAAAAGAAAAAAATCAACTTCAAGACTATATTCAAATAT
GTGCATTCAAGTGGGATTCGAAACATAATCAATCAACAAAATGCAATATACCCCAAGATGAGTGG
TAACAATATGA
Found at i:1848581 original size:18 final size:18
Alignment explanation
Indices: 1848540--1848612 Score: 88
Period size: 18 Copynumber: 4.4 Consensus size: 18
1848530 ACCGGTCACA
1848540 ACCCGACCCGACCCG-TG
1 ACCCGACCCGACCCGTTG
1848557 A-CCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
1848573 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1848587 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1848605 ACCCGACC
1 ACCCGACC
1848613 GTTGACCGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
13 12 0.25
16 13 0.27
17 2 0.04
18 21 0.44
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1848619 original size:12 final size:13
Alignment explanation
Indices: 1848560--1848596 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1848550 ACCCGTGACC
1848560 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1848573 TACCCGACCCGTT
1 GACCCGACCCGTT
1848586 GACCCGACCCG
1 GACCCGACCCG
1848597 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1849949 original size:18 final size:18
Alignment explanation
Indices: 1849923--1849957 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1849913 TCGAAAGGAC
*
1849923 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1849941 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1849958 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1853738 original size:18 final size:18
Alignment explanation
Indices: 1853715--1853789 Score: 106
Period size: 18 Copynumber: 4.4 Consensus size: 18
1853705 GACGGTCACA
1853715 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1853733 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
1853750 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1853764 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1853782 ACCCGACC
1 ACCCGACC
1853790 GTTGACCGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.24
18 38 0.76
ACGTcount: A:0.17, C:0.51, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1853755 original size:31 final size:31
Alignment explanation
Indices: 1853719--1853796 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
1853709 GTCACAACCC
1853719 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
1853750 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
1853781 GACCCGA-CCGTTGACC
1 GACCCGACCCGTTGACC
1853797 GTTGACCCGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 9 0.20
31 36 0.80
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:1853796 original size:12 final size:13
Alignment explanation
Indices: 1853737--1853773 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1853727 CCGTTGACCC
1853737 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1853750 TACCCGACCCGTT
1 GACCCGACCCGTT
1853763 GACCCGACCCG
1 GACCCGACCCG
1853774 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1853798 original size:7 final size:7
Alignment explanation
Indices: 1853786--1853819 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
1853776 CCGTTGACCC
1853786 GACCGTT
1 GACCGTT
1853793 GACCGTT
1 GACCGTT
1853800 GACCCGTT
1 GA-CCGTT
*
1853808 GACCATT
1 GACCGTT
1853815 GACCG
1 GACCG
1853820 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:1853808 original size:15 final size:15
Alignment explanation
Indices: 1853788--1853818 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1853778 GTTGACCCGA
*
1853788 CCGTTGACCGTTGAC
1 CCGTTGACCATTGAC
1853803 CCGTTGACCATTGAC
1 CCGTTGACCATTGAC
1853818 C
1 C
1853819 GGAGTTGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.35, G:0.23, T:0.26
Consensus pattern (15 bp):
CCGTTGACCATTGAC
Found at i:1857737 original size:38 final size:37
Alignment explanation
Indices: 1857674--1857745 Score: 117
Period size: 38 Copynumber: 1.9 Consensus size: 37
1857664 ACTTAACATT
*
1857674 AAATTTTGAACGAGATATTAAAATGAAACAAAAACTA
1 AAATTTTGAACGAAATATTAAAATGAAACAAAAACTA
*
1857711 AAATTTTTAACGATAATATTAAAATGAAACAAAAA
1 AAATTTTGAACGA-AATATTAAAATGAAACAAAAA
1857746 TTACACCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 12 0.38
38 20 0.62
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.26
Consensus pattern (37 bp):
AAATTTTGAACGAAATATTAAAATGAAACAAAAACTA
Found at i:1858383 original size:23 final size:23
Alignment explanation
Indices: 1858357--1858402 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1858347 TTTTTTAATA
*
1858357 ATTTTATTTTTAT-GAAATGTTTT
1 ATTTTACTTTTATAG-AATGTTTT
*
1858380 ATTTTGCTTTTATAGAATGTTTT
1 ATTTTACTTTTATAGAATGTTTT
1858403 TCTTGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.24, C:0.02, G:0.11, T:0.63
Consensus pattern (23 bp):
ATTTTACTTTTATAGAATGTTTT
Found at i:1859915 original size:103 final size:103
Alignment explanation
Indices: 1859744--1859961 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
1859734 TAATGTCCAT
* *
1859744 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1859809 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
1859847 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1859912 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1859950 AAGGACCACATA
1 AAGGACCACATA
1859962 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1862896 original size:20 final size:21
Alignment explanation
Indices: 1862849--1862896 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
1862839 ATGCCACGTG
**
1862849 ATAAATTTTTTAATATTAAAA
1 ATAAATTTTGCAATATTAAAA
1862870 A-ATAATTTTGCAA-ATTAAAA
1 ATA-AATTTTGCAATATTAAAA
1862890 ATAAATT
1 ATAAATT
1862897 AAAATGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
ATAAATTTTGCAATATTAAAA
Found at i:1875068 original size:4 final size:4
Alignment explanation
Indices: 1875053--1875117 Score: 93
Period size: 4 Copynumber: 17.2 Consensus size: 4
1875043 GAACACACAC
*
1875053 ACAT ACAG ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1875099 ACAT --AT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT A
1875118 TACATATACA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 4 0.07
4 51 0.93
ACGTcount: A:0.51, C:0.23, G:0.02, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:1875093 original size:34 final size:34
Alignment explanation
Indices: 1875053--1875117 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
1875043 GAACACACAC
1875053 ACATACAGACATACATATACATACATACATACAT
1 ACATACAGACATACATATACATACATACATACAT
*
1875087 ACATACATACATACATATACATACATACATA
1 ACATACAGACATACATATACATACATACATA
1875118 TACATATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.51, C:0.23, G:0.02, T:0.25
Consensus pattern (34 bp):
ACATACAGACATACATATACATACATACATACAT
Found at i:1875128 original size:12 final size:12
Alignment explanation
Indices: 1875063--1875149 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 12
1875053 ACATACAGAC
1875063 ATACATATACAT
1 ATACATATACAT
1875075 ACATACATACATACAT
1 --ATACAT--ATACAT
* * *
1875091 ACATACATACAT
1 ATACATATACAT
1875103 ATACATACATACAT
1 ATACAT--ATACAT
1875117 ATACATATACAT
1 ATACATATACAT
*
1875129 ATACATATATAT
1 ATACATATACAT
*
1875141 ATATATATA
1 ATACATATA
1875150 TGAAAATCTG
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
12 34 0.56
14 21 0.34
16 6 0.10
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (12 bp):
ATACATATACAT
Found at i:1876502 original size:17 final size:16
Alignment explanation
Indices: 1876480--1876533 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
1876470 AACCGGGTAT
1876480 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
**
1876497 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
1876512 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
1876529 CGGGT
1 CGGGT
1876534 TGGGACACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 11 0.35
16 4 0.13
17 16 0.52
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:1876591 original size:15 final size:16
Alignment explanation
Indices: 1876559--1876613 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
1876549 AAAATCGTCG
*
1876559 ACCCGGAAGTTCCGGGT
1 ACCCGGAA-ATCCGGGT
1876576 ACCCGGAAAT-CGGGT
1 ACCCGGAAATCCGGGT
* *
1876591 ACCTGAAAATCCGGGT
1 ACCCGGAAATCCGGGT
1876607 ACCCGGA
1 ACCCGGA
1876614 TTTGCACACC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 13 0.41
16 11 0.34
17 8 0.25
ACGTcount: A:0.25, C:0.29, G:0.31, T:0.15
Consensus pattern (16 bp):
ACCCGGAAATCCGGGT
Found at i:1879479 original size:183 final size:182
Alignment explanation
Indices: 1879160--1879525 Score: 678
Period size: 183 Copynumber: 2.0 Consensus size: 182
1879150 CAGGCACTTA
*
1879160 TTTCTGATATATTTTAACCATGCTAAATGACATTAAAAGGAATTTGCAGTATACCATTTTCAGCT
1 TTTCTGATATATTTTAACCATGCTAAATGACATTAAAAAGAATTTGCAGTATACCATTTTCAGCT
* *
1879225 CAACAGTTGGTGGTGGTCCTTCGTGACAGAAGCTTAACGTTCGGCTTGCCTTGAATGTCAAGCTC
66 CAACAGTTGGTGGAGGTCCTTCGTAACAGAAGCTTAACGTTCGGCTTGCCTTGAATGTCAAGCTC
1879290 TTTCTGAATTGCCATAGAAACCAACCAACAAAAATGTAGAAAATGGTTATGG
131 TTTCTGAATTGCCATAGAAACCAACCAACAAAAATGTAGAAAATGGTTATGG
1879342 TTTCTGATATATTTTTAACCATGCTAAATGACATTAAAAAGAATTTGCAGTATACCATTTTCAGC
1 TTTCTGATATA-TTTTAACCATGCTAAATGACATTAAAAAGAATTTGCAGTATACCATTTTCAGC
*
1879407 TCAACAGTTGGTGGAGGTCCTTCGTAACAGAAGCTTAACGTTCTGCTTGCCTTGAATGTCAAGCT
65 TCAACAGTTGGTGGAGGTCCTTCGTAACAGAAGCTTAACGTTCGGCTTGCCTTGAATGTCAAGCT
*
1879472 CTTTCTGAATTGCCATAGAAACCAACCAACAAAAATGTAGAGAATGGTTATGG
130 CTTTCTGAATTGCCATAGAAACCAACCAACAAAAATGTAGAAAATGGTTATGG
1879525 T
1 T
1879526 AAATCATAAA
Statistics
Matches: 178, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
182 11 0.06
183 167 0.94
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (182 bp):
TTTCTGATATATTTTAACCATGCTAAATGACATTAAAAAGAATTTGCAGTATACCATTTTCAGCT
CAACAGTTGGTGGAGGTCCTTCGTAACAGAAGCTTAACGTTCGGCTTGCCTTGAATGTCAAGCTC
TTTCTGAATTGCCATAGAAACCAACCAACAAAAATGTAGAAAATGGTTATGG
Found at i:1885712 original size:31 final size:31
Alignment explanation
Indices: 1885676--1885736 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1885666 AAACTTAAAA
*
1885676 TAGTTTTGCAATACTGAAATTTAAATAATTT
1 TAGTTTTACAATACTGAAATTTAAATAATTT
*
1885707 TAGTTTTATAATACTGAAATTTAAATAATT
1 TAGTTTTACAATACTGAAATTTAAATAATT
1885737 CATACAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (31 bp):
TAGTTTTACAATACTGAAATTTAAATAATTT
Found at i:1885788 original size:22 final size:22
Alignment explanation
Indices: 1885760--1885875 Score: 171
Period size: 22 Copynumber: 5.3 Consensus size: 22
1885750 TAATAATTTT
*
1885760 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
1885782 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1885804 TTTTAAAATAAATCAATCCAT-
1 TTTTAAAATAAATCAATCCATA
* *** *
1885825 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
1885847 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1885869 TTTTAAA
1 TTTTAAA
1885876 CATTTCAAAC
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
21 16 0.20
22 66 0.80
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1885847 original size:43 final size:44
Alignment explanation
Indices: 1885760--1885875 Score: 171
Period size: 43 Copynumber: 2.7 Consensus size: 44
1885750 TAATAATTTT
*
1885760 TTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
* *** *
1885804 TTTTAAAATAAATCAATCCAT-TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
1885847 TTTTAAAATAAATCAATCCATATTTTAAA
1 TTTTAAAATAAATCAATCCATATTTTAAA
1885876 CATTTCAAAC
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 38 0.58
44 27 0.42
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (44 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
Found at i:1887360 original size:22 final size:22
Alignment explanation
Indices: 1887332--1887662 Score: 469
Period size: 22 Copynumber: 15.2 Consensus size: 22
1887322 AATCCCAACG
1887332 TAAATCAATCCATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
1887354 TAAATCAATCCATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
*
1887376 TAAATCAATTCATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
*
1887398 TAAATAAATCCATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
1887420 T--A--AATCCATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
1887438 TAAATCAATCCATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
*** *
1887460 TAAATTTTTTCATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
*
1887482 CAAATCAATCCATA-TTTAAAA
1 TAAATCAATCCATATTTTAAAA
*
1887503 TAAATCAATCTATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
1887525 TAAATCAATCAATCCATATTTTAAAA
1 T--A--AATCAATCCATATTTTAAAA
1887551 TAAATCAATCCATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
** *
1887573 TAAAT-TTTTCATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
1887594 T-AATCAATCCATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
1887615 TAAATCAATCCATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
*
1887637 TAAATCAATACATATTTTAAAA
1 TAAATCAATCCATATTTTAAAA
1887659 TAAA
1 TAAA
1887663 ATTTAAAATA
Statistics
Matches: 276, Mismatches: 22, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.06
20 5 0.02
21 47 0.17
22 185 0.67
24 2 0.01
26 20 0.07
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCAATCCATATTTTAAAA
Found at i:1888956 original size:51 final size:49
Alignment explanation
Indices: 1888879--1888987 Score: 191
Period size: 51 Copynumber: 2.2 Consensus size: 49
1888869 ATAAAACACC
1888879 AAAATTGATCGCCTAGGTACTAAACGTGTAATTTACCCCTTTTTACTAATAT
1 AAAA-TGATCGCCTAGGTACTAAACGTGTAATTTACCCCTTTTTACT-A-AT
1888931 AAAATGATCGCCTAGGTACTAAACGTGTAATTTACCCCTTTTTACTAAT
1 AAAATGATCGCCTAGGTACTAAACGTGTAATTTACCCCTTTTTACTAAT
1888980 AAAATGAT
1 AAAATGAT
1888988 TACAATATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
49 10 0.18
50 1 0.02
51 42 0.74
52 4 0.07
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (49 bp):
AAAATGATCGCCTAGGTACTAAACGTGTAATTTACCCCTTTTTACTAAT
Found at i:1895686 original size:21 final size:22
Alignment explanation
Indices: 1895660--1895705 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1895650 TTAATAAAAA
*
1895660 TTATTTAAATTATT-ATTATTT
1 TTATTTAAAATATTAATTATTT
*
1895681 TTATTTAAAATATTAATTTTTT
1 TTATTTAAAATATTAATTATTT
1895703 TTA
1 TTA
1895706 ATATTTATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTTAAAATATTAATTATTT
Found at i:1898804 original size:26 final size:25
Alignment explanation
Indices: 1898773--1898822 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
1898763 ATTTTAACAT
* *
1898773 AAAATATATATTTTTAAATGAAAATA
1 AAAATAAATACTTTTAAAT-AAAATA
1898799 AAAATAAATACTTTTAAATAAAAT
1 AAAATAAATACTTTTAAATAAAAT
1898823 GGTCTCCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
AAAATAAATACTTTTAAATAAAATA
Found at i:1899156 original size:10 final size:10
Alignment explanation
Indices: 1899143--1899175 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1899133 TGTATATAAC
*
1899143 ATATGAAAAA
1 ATATGAAGAA
1899153 ATATGAAGAA
1 ATATGAAGAA
1899163 ATATGAAGAA
1 ATATGAAGAA
1899173 ATA
1 ATA
1899176 CACAAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (10 bp):
ATATGAAGAA
Found at i:1899982 original size:21 final size:22
Alignment explanation
Indices: 1899953--1900005 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1899943 ATTATGACTA
1899953 TCGCATTGCGATTTT-CCAATT
1 TCGCATTGCGATTTTCCCAATT
*
1899974 TCGCGTTGCGATTTTCCCAA-T
1 TCGCATTGCGATTTTCCCAATT
*
1899995 TCGCAATGCGA
1 TCGCATTGCGA
1900006 ATAAGTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCCAATT
Found at i:1900025 original size:41 final size:42
Alignment explanation
Indices: 1899980--1900068 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 42
1899970 AATTTCGCGT
* * *
1899980 TGCGATTTTCCCAATTCGCAATGCGAA-TAAGTAAATCGCAA
1 TGCGATTTTCCAAAATCGCAATGCGAATTAAGAAAATCGCAA
* ** **
1900021 TGCGAATTTGGAAAATCGCAATGCGAATTTGGAAAATCGCAA
1 TGCGATTTTCCAAAATCGCAATGCGAATTAAGAAAATCGCAA
1900063 TGCGAT
1 TGCGAT
1900069 ACTGACTATC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 22 0.58
42 16 0.42
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (42 bp):
TGCGATTTTCCAAAATCGCAATGCGAATTAAGAAAATCGCAA
Found at i:1900038 original size:21 final size:21
Alignment explanation
Indices: 1899995--1900067 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
1899985 TTTTCCCAAT
** *
1899995 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
1900015 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
1900036 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
1900057 TCGCAATGCGA
1 TCGCAATGCGA
1900068 TACTGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 12 0.24
21 37 0.76
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:1900080 original size:41 final size:42
Alignment explanation
Indices: 1900053--1900168 Score: 132
Period size: 41 Copynumber: 2.8 Consensus size: 42
1900043 GCGAATTTGG
*
1900053 AAAATCGCAATGCGATACTGACTATCGCAACGCG-ATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGAATAATAC
* * *
1900094 AAAATCGTAACGCGATACTGACTTTCGCAACGCG-ATACTGAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGAATAAT-AC
** *
1900136 --TTTCGCAACGCGATACTGACTTTCGCAACGCGA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGA
1900169 TACTGACTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 29 0.44
41 35 0.53
42 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.22
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGAATAATAC
Found at i:1900081 original size:20 final size:20
Alignment explanation
Indices: 1900057--1900250 Score: 237
Period size: 20 Copynumber: 9.7 Consensus size: 20
1900047 ATTTGGAAAA
* *
1900057 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
* **
1900077 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
*
1900098 TCGTAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
1900118 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
1900138 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
1900158 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
1900178 TCGCAACGCAATTCTGACTT
1 TCGCAACGCGATACTGACTT
* *
1900198 TCGTAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
* * *
1900218 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATACTGACTT
*
1900238 TCGCAACGAGATA
1 TCGCAACGCGATA
1900251 ATACAGAATC
Statistics
Matches: 155, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
19 2 0.01
20 137 0.88
21 14 0.09
22 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:1900423 original size:12 final size:12
Alignment explanation
Indices: 1900404--1900437 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1900394 CTCTCCGGCG
1900404 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1900416 ATATCCGTTCCT
1 ACATCCGTTCCT
1900428 ACATCC-TTCC
1 ACATCCGTTCC
1900438 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1901614 original size:21 final size:21
Alignment explanation
Indices: 1901585--1901645 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1901575 GAACGGTGGG
*
1901585 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
1901606 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
1901627 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
1901646 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:1902516 original size:30 final size:30
Alignment explanation
Indices: 1902460--1902667 Score: 338
Period size: 30 Copynumber: 7.1 Consensus size: 30
1902450 GAAAGACCTA
* * *
1902460 TCCAGAGGTCACACAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1902489 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1902519 TCCAGAGGTCATAAAGATCCTCGGTAAC--
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1902547 T--AG-GGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1902574 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1902604 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
1902634 TCCAGAGGTCATAAAGATCCTCGGTAATTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1902664 TCCA
1 TCCA
1902668 TATGTTCCTT
Statistics
Matches: 169, Mismatches: 4, Indels: 11
0.92 0.02 0.06
Matches are distributed among these distances:
25 22 0.13
26 2 0.01
27 1 0.01
28 1 0.01
29 17 0.10
30 126 0.75
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1902580 original size:85 final size:88
Alignment explanation
Indices: 1902462--1902667 Score: 330
Period size: 85 Copynumber: 2.4 Consensus size: 88
1902452 AAGACCTATC
* * *
1902462 CAGAGGTCACACAGA-CCCCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAG
1 CAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAG
1902526 GTCATAAAGATCCTCGGTAAC-T
66 GTCATAAAGATCCTCGGTAACGT
1902548 -AG-GGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAG
1 CAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAG
1902611 GTCATAAAGATCCTCGGTAACTGT
66 GTCATAAAGATCCTCGGTAAC-GT
*
1902635 CCAGAGGTCATAAAGATCCTCGGTAATTGTCCA
1 -CAGAGGTCATAAAGATCCTCGGTAACTGTCCA
1902668 TATGTTCCTT
Statistics
Matches: 110, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
84 9 0.08
85 71 0.65
87 1 0.01
89 2 0.02
90 27 0.25
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (88 bp):
CAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAG
GTCATAAAGATCCTCGGTAACGT
Found at i:1902699 original size:29 final size:30
Alignment explanation
Indices: 1902656--1902751 Score: 99
Period size: 29 Copynumber: 3.2 Consensus size: 30
1902646 AAAGATCCTC
* *
1902656 GGTAATTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
1902686 GGTAA-TGTCCATATGTCTCGAAAG-ACATA
1 GGTAACTGTCCATATGT-TCCATAGAACATA
*
1902715 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
1902747 -GTAAC
1 GGTAAC
1902752 CCTCGACTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
29 22 0.40
30 9 0.16
31 8 0.15
32 16 0.29
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:1903927 original size:21 final size:21
Alignment explanation
Indices: 1903903--1903947 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1903893 TCTTGTTCGT
* *
1903903 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1903924 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1903945 TTG
1 TTG
1903948 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1907181 original size:29 final size:30
Alignment explanation
Indices: 1907068--1907276 Score: 331
Period size: 29 Copynumber: 7.1 Consensus size: 30
1907058 GAAGGACCTA
* * *
1907068 TCCAGAGGTCACACAGA-CC-CCGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1907096 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
1907127 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1907157 TCCAGAGGTCA-AAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1907186 TCCAGAGGTCAT-AAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
1907215 TCCATAGG-CAT-AAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1907243 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1907273 TCCA
1 TCCA
1907277 TATGTTCCTT
Statistics
Matches: 170, Mismatches: 5, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
28 42 0.25
29 58 0.34
30 40 0.24
31 30 0.18
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1907309 original size:31 final size:32
Alignment explanation
Indices: 1907271--1907363 Score: 118
Period size: 31 Copynumber: 2.9 Consensus size: 32
1907261 CCTCGGTAAC
* *
1907271 TGTCCATATGTTCCTTAGAACATAGGTATAA-
1 TGTCCATATGTTCCATAGAACATAGGTAAAAT
* *
1907302 TGTCCATATGTCTCGAAAG-ACATAGGTAAAAT
1 TGTCCATATGT-TCCATAGAACATAGGTAAAAT
*
1907334 TGTCCATATGTTCCGTAGAACATAGGTAAA
1 TGTCCATATGTTCCATAGAACATAGGTAAA
1907364 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
31 26 0.50
32 26 0.50
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (32 bp):
TGTCCATATGTTCCATAGAACATAGGTAAAAT
Found at i:1907357 original size:32 final size:31
Alignment explanation
Indices: 1907271--1907363 Score: 118
Period size: 32 Copynumber: 3.0 Consensus size: 31
1907261 CCTCGGTAAC
* *
1907271 TGTCCATATGTTCCTTAGAACATAGGTATAA
1 TGTCCATATGTTCCGTAGAACATAGGTAAAA
*
1907302 TGTCCATATG-TCTCG-AAAGACATAGGTAAAA
1 TGTCCATATGTTC-CGTAGA-ACATAGGTAAAA
1907333 TTGTCCATATGTTCCGTAGAACATAGGTAAA
1 -TGTCCATATGTTCCGTAGAACATAGGTAAA
1907364 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
30 4 0.08
31 22 0.42
32 23 0.43
33 4 0.08
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (31 bp):
TGTCCATATGTTCCGTAGAACATAGGTAAAA
Done.