Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008670.1 Hibiscus syriacus cultivar Beakdansim tig00111678_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: 969061
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 5 of 5
Found at i:885461 original size:43 final size:42
Alignment explanation
Indices: 885385--885478 Score: 125
Period size: 43 Copynumber: 2.2 Consensus size: 42
885375 TCGACGGGAA
885385 ATTCGTTTATTTATTAACGTACAAACAAAAATTAGATTCTAT
1 ATTCGTTTATTTATTAACGTACAAACAAAAATTAGATTCTAT
* * * ** *
885427 GTTCGTTTATTTATTAAACGTACGAATATGAATTAGATTTTAT
1 ATTCGTTTATTTATT-AACGTACAAACAAAAATTAGATTCTAT
885470 ATTCGTTTA
1 ATTCGTTTA
885479 ATTAAATGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 14 0.32
43 30 0.68
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.45
Consensus pattern (42 bp):
ATTCGTTTATTTATTAACGTACAAACAAAAATTAGATTCTAT
Found at i:885561 original size:14 final size:14
Alignment explanation
Indices: 885542--885570 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
885532 CGTGTGATAA
885542 TTCATTCATTTATG
1 TTCATTCATTTATG
885556 TTCATTCATTTATG
1 TTCATTCATTTATG
885570 T
1 T
885571 AGAGTTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (14 bp):
TTCATTCATTTATG
Found at i:886701 original size:85 final size:85
Alignment explanation
Indices: 886596--886851 Score: 444
Period size: 86 Copynumber: 3.0 Consensus size: 85
886586 TTAATACTAC
886596 ACAAGGAAAATGATCCTTACAAGAACTTTAAAAAAAAGGTACCTTACCTTAACTAGGACACCTAC
1 ACAAGGAAAATGATCCTTACAAGAACTTTAAAAAAAAGGTACCTTACCTTAACTAGGACACCTAC
886661 CCACAATAAAATCAAACCCA
66 CCACAATAAAATCAAACCCA
*
886681 ACAAGGAAAATGATCCTTACAAGAACTTTAAAAAAAAAGGTACCTTACCTTAACTTGGACACCTA
1 ACAAGGAAAATGATCCTTACAAGAACTTT-AAAAAAAAGGTACCTTACCTTAACTAGGACACCTA
886746 CCCACAATAAAATCAAACCCA
65 CCCACAATAAAATCAAACCCA
* * *
886767 ACAAGGAAAATGATCCTTACAATAACTTTAAAAGAAAGGTGCCTTACCTTAACTA-GACACCTAC
1 ACAAGGAAAATGATCCTTACAAGAACTTTAAAAAAAAGGTACCTTACCTTAACTAGGACACCTAC
886831 CC-CAAATAAAATCAAACCCA
66 CCAC-AATAAAATCAAACCCA
886851 A
1 A
886852 AAATGACAAA
Statistics
Matches: 164, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
83 1 0.01
84 28 0.17
85 52 0.32
86 83 0.51
ACGTcount: A:0.46, C:0.25, G:0.09, T:0.20
Consensus pattern (85 bp):
ACAAGGAAAATGATCCTTACAAGAACTTTAAAAAAAAGGTACCTTACCTTAACTAGGACACCTAC
CCACAATAAAATCAAACCCA
Found at i:887805 original size:23 final size:23
Alignment explanation
Indices: 887779--887839 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
887769 CTCATATAAA
*
887779 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
887802 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
887825 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
887840 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:888026 original size:103 final size:103
Alignment explanation
Indices: 887855--888072 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
887845 TAATGTCCAT
* *
887855 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
887920 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
887958 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
888023 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
888061 AAGGACCACATA
1 AAGGACCACATA
888073 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:889277 original size:21 final size:21
Alignment explanation
Indices: 889251--889294 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
889241 TTTTTATTCG
* *
889251 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
889272 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
889293 CT
1 CT
889295 AGCCCAGAAT
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:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:893095 original size:23 final size:23
Alignment explanation
Indices: 893066--893126 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
893056 CTCATATAAA
*
893066 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* * *
893089 TGTACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
893112 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
893127 TATAATAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:893313 original size:103 final size:103
Alignment explanation
Indices: 893142--893359 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
893132 TAATGTCCAT
* *
893142 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
893207 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
893245 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
893310 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
893348 AAGGACCACATA
1 AAGGACCACATA
893360 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:894565 original size:21 final size:21
Alignment explanation
Indices: 894539--894582 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
894529 TTTTTATTCG
* *
894539 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
894560 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
894581 CT
1 CT
894583 AGCCCAGAAT
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:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:904881 original size:36 final size:36
Alignment explanation
Indices: 904830--904924 Score: 122
Period size: 36 Copynumber: 2.6 Consensus size: 36
904820 CTAGAGATGA
* *
904830 AATTGTTCCACCTCAAACGAAACCACTGAATAACG-
1 AATTGTTCCATCTCAAACGAAACCACCGAATAACGT
904865 AGATTGTTCCATCTCAAAC-ATAACCACCGAATAACGT
1 A-ATTGTTCCATCTCAAACGA-AACCACCGAATAACGT
* *
904902 AATTGGTCAATCTCAAACGAAAC
1 AATTGTTCCATCTCAAACGAAAC
904925 AACTAGTACC
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
35 2 0.04
36 48 0.92
37 2 0.04
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.22
Consensus pattern (36 bp):
AATTGTTCCATCTCAAACGAAACCACCGAATAACGT
Found at i:908957 original size:36 final size:36
Alignment explanation
Indices: 908893--908987 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
908883 GGTACTAGTT
* * *
908893 GTTCCGTTTGAGATGGATCAATTACGTTATTCGGTG
1 GTTCCGTTTGAGATGAAACAATTACGTTATTCGGTA
* *
908929 GTTCCGTTTGGGATGAAACAA-TATCGTTATTTGGTA
1 GTTCCGTTTGAGATGAAACAATTA-CGTTATTCGGTA
* *
908965 GTTCCGTTTGAGGTGGAACAATT
1 GTTCCGTTTGAGATGAAACAATT
908988 TCATCTCTAG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
35 2 0.04
36 46 0.94
37 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (36 bp):
GTTCCGTTTGAGATGAAACAATTACGTTATTCGGTA
Found at i:911729 original size:36 final size:35
Alignment explanation
Indices: 911665--911759 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 35
911655 AGCACTAGTT
* *
911665 GTTCCGTTTGAGAT-GAATCAATTACATTATTCGGTG
1 GTTCCGTTTGGGATGGAA-CAATT-CATTATTCGATG
**
911701 GTTCCGTTTGGGATGGAACAATCTCATTATTTTATG
1 GTTCCGTTTGGGATGGAACAAT-TCATTATTCGATG
*
911737 GTTCTGTTTGAGG-TGGAACAATT
1 GTTCCGTTTG-GGATGGAACAATT
911760 TCATCTCTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
35 1 0.02
36 44 0.86
37 6 0.12
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (35 bp):
GTTCCGTTTGGGATGGAACAATTCATTATTCGATG
Found at i:914489 original size:36 final size:36
Alignment explanation
Indices: 914438--914521 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 36
914428 GGTACTAGTA
* * *
914438 GTTCCGTTTGAGATGAATCAAT-TACGTTATTCGGTG
1 GTTCCGTTTGGGATGAAACAATCT-CATTATTCGGTG
*
914474 GTTCCGTTTGGGATGAAACAATCTCATTATTTGGTG
1 GTTCCGTTTGGGATGAAACAATCTCATTATTCGGTG
*
914510 GTTCTGTTTGGG
1 GTTCCGTTTGGG
914522 GTTGAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 41 0.98
37 1 0.02
ACGTcount: A:0.19, C:0.13, G:0.27, T:0.40
Consensus pattern (36 bp):
GTTCCGTTTGGGATGAAACAATCTCATTATTCGGTG
Found at i:921555 original size:36 final size:36
Alignment explanation
Indices: 921506--921597 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 36
921496 ATACTAGTTG
*
921506 TTCGTTTAAGATGGATCAAT-TACGTTATTCGGTGGT
1 TTCGTTTAAGATGGAACAATCT-CGTTATTCGGTGGT
** *
921542 TTCGTTTGGGATGGAACAATCTCGTTATTTGGTGG-
1 TTCGTTTAAGATGGAACAATCTCGTTATTCGGTGGT
* *
921577 TTCTGTTTGAGGTGGAACAAT
1 TTC-GTTTAAGATGGAACAAT
921598 TTCATCTCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
35 3 0.06
36 44 0.92
37 1 0.02
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.40
Consensus pattern (36 bp):
TTCGTTTAAGATGGAACAATCTCGTTATTCGGTGGT
Found at i:927090 original size:19 final size:19
Alignment explanation
Indices: 927066--927106 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
927056 AAGGTATTGG
927066 TAATGATAAT-AATAATAAT
1 TAATGATAATAAATAAT-AT
927085 TAATGATAATAAATAATAT
1 TAATGATAATAAATAATAT
927104 TAA
1 TAA
927107 AATAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (19 bp):
TAATGATAATAAATAATAT
Found at i:930075 original size:60 final size:60
Alignment explanation
Indices: 930004--930117 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
929994 GTTAATAAAA
* * **
930004 CTTTAGGTCCCTAAACTTTTAATATTTCTCAATTTAGCTCGTAAGCATGTTTCTTTGTTT
1 CTTTAGATCCCTAAACTCTTAATATTTCTCAATTTAGCTCACAAGCATGTTTCTTTGTTT
* *
930064 CTTTAGATCCCTAGACTCTTAATATTTCTCAATTTAGCTCACAAGCTTGTTTCT
1 CTTTAGATCCCTAAACTCTTAATATTTCTCAATTTAGCTCACAAGCATGTTTCT
930118 ATATTTTACA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.46
Consensus pattern (60 bp):
CTTTAGATCCCTAAACTCTTAATATTTCTCAATTTAGCTCACAAGCATGTTTCTTTGTTT
Found at i:931182 original size:137 final size:137
Alignment explanation
Indices: 930936--931338 Score: 725
Period size: 137 Copynumber: 2.9 Consensus size: 137
930926 GACTCGTGCT
* * *
930936 TTCTCACGATATCTACTTCTTGTCATAAAATAAATATTGGTTAAATGATAGTCCTCTTACAATTG
1 TTCTCACGATATCTACTTCTTGTCATAAAATAAATATTGGTTAAATGATCGTCATCTTACGATTG
*
931001 TAATTCTATACCCAAATTAGAATGAAATGATCAACAAAATAAACTTATTGGCTTAACAAATACTT
66 TAATTCTATACCCAAACTAGAATGAAATGATCAACAAAATAAACTTATTGGCTTAACAAATACTT
931066 ATTGTAA
131 ATTGTAA
931073 TTCTCACGATATCTACTTCTTGTCATAAAATAAATATTGGTTAAATGATCGTCATCTTACGATTG
1 TTCTCACGATATCTACTTCTTGTCATAAAATAAATATTGGTTAAATGATCGTCATCTTACGATTG
* *
931138 TAATTCTATTCCCATACTAGAATGAAATGATCAACAAAATAAACTTATTGGCTTAACAAATACTT
66 TAATTCTATACCCAAACTAGAATGAAATGATCAACAAAATAAACTTATTGGCTTAACAAATACTT
931203 ATTGTAA
131 ATTGTAA
* * *
931210 TTCTCACGATATCTACTTCTTATCATAAAATAAATATTGGTTAAATGAACGTCTTCTTACGATTG
1 TTCTCACGATATCTACTTCTTGTCATAAAATAAATATTGGTTAAATGATCGTCATCTTACGATTG
931275 TAATTCTATACCCAAACTAGAATGAAATGATCAACAAAATAAACTTATTGGCTTAACAAATACT
66 TAATTCTATACCCAAACTAGAATGAAATGATCAACAAAATAAACTTATTGGCTTAACAAATACT
931339 AATATTATAT
Statistics
Matches: 255, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 255 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (137 bp):
TTCTCACGATATCTACTTCTTGTCATAAAATAAATATTGGTTAAATGATCGTCATCTTACGATTG
TAATTCTATACCCAAACTAGAATGAAATGATCAACAAAATAAACTTATTGGCTTAACAAATACTT
ATTGTAA
Found at i:933418 original size:27 final size:27
Alignment explanation
Indices: 933388--933441 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
933378 ACCTTAAAAG
933388 ATAGTTTAGTAGTTAAAGTAAAAGCAA
1 ATAGTTTAGTAGTTAAAGTAAAAGCAA
933415 ATAGTTTAGTAGTTAAAGTAAAAGCAA
1 ATAGTTTAGTAGTTAAAGTAAAAGCAA
933442 CCTAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.19, T:0.30
Consensus pattern (27 bp):
ATAGTTTAGTAGTTAAAGTAAAAGCAA
Found at i:933508 original size:72 final size:72
Alignment explanation
Indices: 933419--933604 Score: 318
Period size: 72 Copynumber: 2.6 Consensus size: 72
933409 AAGCAAATAG
*
933419 TTTAGTAGTTAAAGTAAAAGCAACCTAAAAATTTAGTGACTAAATTAAAAACTATAAGATGAGTT
1 TTTATTAGTTAAAGTAAAAGCAACCTAAAAATTTAGTGACTAAATTAAAAACTATAAGATGAGTT
933484 TTAGAAA
66 TTAGAAA
* *
933491 TTTATTAGTTAAAGTAAAAGCAACCTTAAAATTTAGTGACTAAATTAAAAATTATAAGATGAGTT
1 TTTATTAGTTAAAGTAAAAGCAACCTAAAAATTTAGTGACTAAATTAAAAACTATAAGATGAGTT
933556 TTAGAAA
66 TTAGAAA
* * *
933563 TTTATTAGTTAAAGTAAAAGAAACCTAAAATTTTAATGACTA
1 TTTATTAGTTAAAGTAAAAGCAACCTAAAAATTTAGTGACTA
933605 CCAAAGGAGT
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 107 1.00
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (72 bp):
TTTATTAGTTAAAGTAAAAGCAACCTAAAAATTTAGTGACTAAATTAAAAACTATAAGATGAGTT
TTAGAAA
Found at i:935651 original size:4 final size:4
Alignment explanation
Indices: 935642--935679 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
935632 TATATAAGTC
*
935642 AATA AATA AATA AACTT AA-A AATA AATA AATA AATA AA
1 AATA AATA AATA AA-TA AATA AATA AATA AATA AATA AA
935680 CGAACTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 2 0.07
4 25 0.83
5 3 0.10
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:936215 original size:23 final size:23
Alignment explanation
Indices: 936173--936216 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
936163 AGCTCGAGAC
* * *
936173 TTGAGCTCGATTGAAGCTCGATT
1 TTGAGCTCAATTCAACCTCGATT
936196 TTGAGCTCAATTCAACCTCGA
1 TTGAGCTCAATTCAACCTCGA
936217 CGGGTTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (23 bp):
TTGAGCTCAATTCAACCTCGATT
Found at i:942538 original size:20 final size:23
Alignment explanation
Indices: 942496--942544 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 23
942486 CAATTGATAT
942496 AATTT-TTTAATTATTAGACTTA
1 AATTTATTTAATTATTAGACTTA
942518 AATTTATTTAATTA-TA-A-TTA
1 AATTTATTTAATTATTAGACTTA
942538 AATTTAT
1 AATTTAT
942545 AAAATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.38
21 1 0.04
22 7 0.27
23 8 0.31
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
AATTTATTTAATTATTAGACTTA
Found at i:942550 original size:20 final size:21
Alignment explanation
Indices: 942515--942555 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
942505 ATTATTAGAC
**
942515 TTAAATTTATTTAA-TTATAA
1 TTAAATTTATAAAATTTATAA
942535 TTAAATTTATAAAATTTATAA
1 TTAAATTTATAAAATTTATAA
942556 ATTTTAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAATTTATAAAATTTATAA
Found at i:942558 original size:17 final size:17
Alignment explanation
Indices: 942536--942568 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
942526 TAATTATAAT
942536 TAAATTTATAA-AATTTA
1 TAAATTT-TAAGAATTTA
942553 TAAATTTTAAGAATTT
1 TAAATTTTAAGAATTT
942569 TTTGTTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TAAATTTTAAGAATTTA
Found at i:944651 original size:5 final size:5
Alignment explanation
Indices: 944644--944727 Score: 143
Period size: 5 Copynumber: 17.0 Consensus size: 5
944634 GTCCGTCCGT
* *
944644 CTCGT CTCGG CTCGT CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
944694 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG -TCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
944728 TCGTGGTCGT
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
4 4 0.05
5 72 0.95
ACGTcount: A:0.00, C:0.39, G:0.38, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:944737 original size:6 final size:6
Alignment explanation
Indices: 944726--944764 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
944716 CGGCTCGGTC
944726 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
944765 AATGCGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:945061 original size:22 final size:22
Alignment explanation
Indices: 945036--945090 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
945026 TCAGGAGTTA
* *
945036 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
945058 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
945080 CGGGAGTTATA
1 CAGGAGTTATA
945091 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:950627 original size:5 final size:5
Alignment explanation
Indices: 950613--950661 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
950603 GTCCGTCCGT
* * * *
950613 CTCGT CTCGG CTCGG CACGA CACGG CTCGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
950662 TGGTCGTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.06, C:0.41, G:0.35, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:950670 original size:6 final size:6
Alignment explanation
Indices: 950659--950713 Score: 83
Period size: 6 Copynumber: 9.2 Consensus size: 6
950649 TCGGCTCGGC
* * *
950659 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
950707 TCGTGG T
1 TCGTGG T
950714 AATACGTGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.05, C:0.16, G:0.49, T:0.29
Consensus pattern (6 bp):
TCGTGG
Found at i:956576 original size:5 final size:5
Alignment explanation
Indices: 956562--956610 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
956552 GTCCGTCCGT
* * * *
956562 CTCGT CTCGG CTCGG CACGA CACGG CTCGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
956611 TGGTCGTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.06, C:0.41, G:0.35, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:956619 original size:6 final size:6
Alignment explanation
Indices: 956608--956662 Score: 83
Period size: 6 Copynumber: 9.2 Consensus size: 6
956598 TCGGCTCGGC
* * *
956608 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
956656 TCGTGG T
1 TCGTGG T
956663 AATACGTGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.05, C:0.16, G:0.49, T:0.29
Consensus pattern (6 bp):
TCGTGG
Found at i:956959 original size:21 final size:22
Alignment explanation
Indices: 956935--956988 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
956925 TCAGGAGTTA
*
956935 CAGGAGTTATTTGAT-TAATTC
1 CAGGAGTTATATGATATAATTC
* * *
956956 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
956978 CGGGAGTTATA
1 CAGGAGTTATA
956989 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:962503 original size:5 final size:5
Alignment explanation
Indices: 962489--962537 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
962479 GTCCGTCCGT
* * * *
962489 CTCGT CTCGG CTCGG CACGA CACGG CTCGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
962538 TGGTCGTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.06, C:0.41, G:0.35, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:962546 original size:6 final size:6
Alignment explanation
Indices: 962535--962595 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
962525 TCGGCTCGGC
* * * *
962535 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
962583 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
962596 AATACGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.07, C:0.16, G:0.49, T:0.28
Consensus pattern (6 bp):
TCGTGG
Found at i:962890 original size:22 final size:22
Alignment explanation
Indices: 962865--962918 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
962855 TCAGGAGTTA
* *
962865 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* *
962887 CAGG-GTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
962908 CGGGAGTTATA
1 CAGGAGTTATA
962919 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Done.