Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009074.1 Hibiscus syriacus cultivar Beakdansim tig00112507_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: 2143704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1524769 original size:147 final size:146
Alignment explanation
Indices: 1524583--1524877 Score: 556
Period size: 147 Copynumber: 2.0 Consensus size: 146
1524573 ATTCATTTTT
1524583 TGAATTTAAAACACTTTTTTTTCTTTTCGTTTAACTAAAACACCTACACCACTTATCCCTTATTT
1 TGAATTTAAAACACTTTTTTTTCTTTTCGTTTAACTAAAACACCTACACCACTTATCCCTTATTT
1524648 TAATTACCCAACCAATTTCACTCGAATTAAAATACCCT-CCCACATCCCCTTCTATTAGAACCCA
66 TAATTACCCAACCAATTTCACTCGAATTAAAATACCCTCCCCACATCCCCTTCTATTAGAACCCA
1524712 ACACATTCATCTTCCC
131 ACACATTCATCTTCCC
1524728 TGAATTTAAAACACTTTTTTTTTTCTTTTCGTTTAACTAAAACACCTACACCACTTATCCCTTAT
1 TGAATTTAAAACAC--TTTTTTTTCTTTTCGTTTAACTAAAACACCTACACCACTTATCCCTTAT
1524793 TTTAATTACCCAACCAATTTCACTCGAATTAAAATACCCTCCCCCACATCCCCTTCTATTAGAAC
64 TTTAATTACCCAACCAATTTCACTCGAATTAAAATACCCT-CCCCACATCCCCTTCTATTAGAAC
1524858 CCAACACATTCATCTTCCC
128 CCAACACATTCATCTTCCC
1524877 T
1 T
1524878 AAACTGTTAC
Statistics
Matches: 146, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
145 14 0.10
147 89 0.61
149 43 0.29
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.36
Consensus pattern (146 bp):
TGAATTTAAAACACTTTTTTTTCTTTTCGTTTAACTAAAACACCTACACCACTTATCCCTTATTT
TAATTACCCAACCAATTTCACTCGAATTAAAATACCCTCCCCACATCCCCTTCTATTAGAACCCA
ACACATTCATCTTCCC
Found at i:1531458 original size:117 final size:117
Alignment explanation
Indices: 1531252--1531484 Score: 457
Period size: 117 Copynumber: 2.0 Consensus size: 117
1531242 TCCACGGCCG
1531252 CCAGCCTTCTCATTGTGTTCCATGTATTCAACGACATCAGACAATACTCTGGAGGTAAATTCTGA
1 CCAGCCTTCTCATTGTGTTCCATGTATTCAACGACATCAGACAATACTCTGGAGGTAAATTCTGA
*
1531317 TCCTATTTTCATTCAACCATTACTAACGTACCTTCCGATTTATGATTTTAAT
66 TCCTATTTTCATTCAACCATTACTAACGTACCTTACGATTTATGATTTTAAT
1531369 CCAGCCTTCTCATTGTGTTCCATGTATTCAACGACATCAGACAATACTCTGGAGGTAAATTCTGA
1 CCAGCCTTCTCATTGTGTTCCATGTATTCAACGACATCAGACAATACTCTGGAGGTAAATTCTGA
1531434 TCCTATTTTCATTCAACCATTACTAACGTACCTTACGATTTATGATTTTAA
66 TCCTATTTTCATTCAACCATTACTAACGTACCTTACGATTTATGATTTTAA
1531485 ATAGGATTTC
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 115 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (117 bp):
CCAGCCTTCTCATTGTGTTCCATGTATTCAACGACATCAGACAATACTCTGGAGGTAAATTCTGA
TCCTATTTTCATTCAACCATTACTAACGTACCTTACGATTTATGATTTTAAT
Found at i:1535949 original size:17 final size:17
Alignment explanation
Indices: 1535927--1535961 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1535917 GGGGAAATAG
1535927 TATCTTACGTTATCGGT
1 TATCTTACGTTATCGGT
*
1535944 TATCTTACGTTATTGGT
1 TATCTTACGTTATCGGT
1535961 T
1 T
1535962 TAAGTCCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.51
Consensus pattern (17 bp):
TATCTTACGTTATCGGT
Found at i:1536236 original size:13 final size:13
Alignment explanation
Indices: 1536220--1536262 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1536210 TTATTTTATA
1536220 TATGTATTAAAAT
1 TATGTATTAAAAT
**
1536233 TATGTCAACAAAAT
1 TATGT-ATTAAAAT
1536247 ATATGTATTAAAAT
1 -TATGTATTAAAAT
1536261 TA
1 TA
1536263 ACCGAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 7 0.29
14 12 0.50
15 5 0.21
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (13 bp):
TATGTATTAAAAT
Found at i:1538659 original size:29 final size:29
Alignment explanation
Indices: 1538626--1538690 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1538616 TTACCAATGT
* *
1538626 ATTTTTTAGTATTTGTTATTAAAGG-CTCA
1 ATTTTTTAATATTTATTATTAAAGGTC-CA
* *
1538655 ATTTTTCAATATTTATTATTAGAGGTCCA
1 ATTTTTTAATATTTATTATTAAAGGTCCA
1538684 ATTTTTT
1 ATTTTTT
1538691 TTCAATATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.54
Consensus pattern (29 bp):
ATTTTTTAATATTTATTATTAAAGGTCCA
Found at i:1539984 original size:3 final size:3
Alignment explanation
Indices: 1539976--1540022 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
1539966 TACTGTTAAA
* *
1539976 ATT ATT ATT ATT ATT ATT AAAT ATT ATT ATT ATT ATG ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
1540022 A
1 A
1540023 AATAAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1540004 original size:22 final size:21
Alignment explanation
Indices: 1539971--1540016 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
1539961 CATTCTACTG
*
1539971 TTAAAATTATTATTATTATTA
1 TTAAAATTATTATTATTATGA
1539992 TTAAATATTATTATTATTATGA
1 TTAAA-ATTATTATTATTATGA
1540014 TTA
1 TTA
1540017 TTATTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAAAATTATTATTATTATGA
Found at i:1541422 original size:17 final size:17
Alignment explanation
Indices: 1541391--1541437 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
1541381 TAACAGTTTG
1541391 ATATTTT-CA-TTTAAT
1 ATATTTTGCATTTTAAT
1541406 ATATTTTGCATTTTAAT
1 ATATTTTGCATTTTAAT
*
1541423 AT-TATTGC-TTTTAAT
1 ATATTTTGCATTTTAAT
1541438 TTCTTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 14 0.48
16 7 0.24
17 8 0.28
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (17 bp):
ATATTTTGCATTTTAAT
Found at i:1542753 original size:490 final size:491
Alignment explanation
Indices: 1541833--1542815 Score: 1941
Period size: 490 Copynumber: 2.0 Consensus size: 491
1541823 CGAGAAGGAA
1541833 TAAAGTCAAATGGGTTAAAACCTAAACTAAGGCAATACTACTCCGATACCCTAGTTCTAAGCCGT
1 TAAAGTCAAATGGGTTAAAACCTAAACTAAGGCAATACTACTCCGATACCCTAGTTCTAAGCCGT
1541898 CATAAATTCCAATGACAAAAACGCATAAAAAGTAGAAGCCATGGAAATTACTACAAAGGCATTAA
66 CATAAATTCCAATGACAAAAACGCATAAAAAGTAGAAGCCATGGAAATTACTACAAAGGCATTAA
1541963 AAGAAGACAGAAATGATACACCCTATAGATGTGACCTGCACTACTCGGGTACCCTGGTCTTAACT
131 AAGAAGACAGAAATGATACACCCTATAGATGTGACCTGCACTACTCGGGTACCCTGGTCTTAACT
1542028 CTCCATACTTTCCTATCAGAGGTCATGTCCTCGGTAAGTGCTAAATCCTTCAAATCAGATCTCAA
196 CTCCATACTTTCCTATCAGAGGTCATGTCCTCGGTAAGTGCTAAATCCTTCAAATCAGATCTCAA
1542093 GCAGTCTTCCCACTTCCGCCTTGGTCGTCCTCTCCTTCTGGAGCCGTCAACTGTAATCGACTCTA
261 GCAGTCTTCCCACTTCCGCCTTGGTCGTCCTCTCCTTCTGGAGCCGTCAACTGTAATCGACTCTA
1542158 CCATCTTGACCGCATCTGACGGTTGTCGCCTAAAGACATGCCCAAACCACCGTAGTCTTCTCTCC
326 CCATCTTGACCGCATCTGACGGTTGTCGCCTAAAGACATGCCCAAACCACCGTAGTCTTCTCTCC
*
1542223 CTCAATTTTTCGAATACATGCACCACTCCCAAGGACTTCCTAATAGCAGAG-TTGGTGTCATGTC
391 CTCAATTTTTCGAATACAGGCACCACTCCCAAGGACTTCCTAATAGCAGAGTTTGGTGTCATGTC
1542287 TCACAGAGTCCTACCGCATGCCCATCGAAGCATTCT
456 TCACAGAGTCCTACCGCATGCCCATCGAAGCATTCT
1542323 TAAAGTCAAATGGGTTAAAACCTAAACTAAGGCAATACTACTCCGATACCCTAGTTCTAAGCCGT
1 TAAAGTCAAATGGGTTAAAACCTAAACTAAGGCAATACTACTCCGATACCCTAGTTCTAAGCCGT
*
1542388 CATAAATTCCAATGACAAAAACGTATAAAAAGTAGAAGCCATGGAAATTACTACAAAGGCATTAA
66 CATAAATTCCAATGACAAAAACGCATAAAAAGTAGAAGCCATGGAAATTACTACAAAGGCATTAA
1542453 AAGAAGACAGAAATGATACACCCTATAGATGTGACCTGCACTACTCGGGTACCCTGGTCTTAACT
131 AAGAAGACAGAAATGATACACCCTATAGATGTGACCTGCACTACTCGGGTACCCTGGTCTTAACT
1542518 CTCCATACTTTCCTATCAGAGGTCATGTCCTCGGTAAGTGCTAAATCCTTCAAATCAGATCTCAA
196 CTCCATACTTTCCTATCAGAGGTCATGTCCTCGGTAAGTGCTAAATCCTTCAAATCAGATCTCAA
1542583 GCAGTCTTCCCACTTCCGCCTTGGTCGTCCTCTCCTTCTGGAGCCGTCAACTGTAATCGACTCTA
261 GCAGTCTTCCCACTTCCGCCTTGGTCGTCCTCTCCTTCTGGAGCCGTCAACTGTAATCGACTCTA
1542648 CCATCTTGACCGCATCTGACGGTTGTCGCCTAAAGACATGCCCAAACCACCGTAGTCTTCTCTCC
326 CCATCTTGACCGCATCTGACGGTTGTCGCCTAAAGACATGCCCAAACCACCGTAGTCTTCTCTCC
1542713 CTCAATTTTTCGAATACAGGCACCACTCCCAAGGACTTCCTAATAGCAGAGTTTGGTGTCATGTC
391 CTCAATTTTTCGAATACAGGCACCACTCCCAAGGACTTCCTAATAGCAGAGTTTGGTGTCATGTC
1542778 TCACAGAGTCCTACCGCATGCCCATCGAAGCATTCT
456 TCACAGAGTCCTACCGCATGCCCATCGAAGCATTCT
1542814 TA
1 TA
1542816 TTTATGCGGT
Statistics
Matches: 490, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
490 439 0.90
491 51 0.10
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (491 bp):
TAAAGTCAAATGGGTTAAAACCTAAACTAAGGCAATACTACTCCGATACCCTAGTTCTAAGCCGT
CATAAATTCCAATGACAAAAACGCATAAAAAGTAGAAGCCATGGAAATTACTACAAAGGCATTAA
AAGAAGACAGAAATGATACACCCTATAGATGTGACCTGCACTACTCGGGTACCCTGGTCTTAACT
CTCCATACTTTCCTATCAGAGGTCATGTCCTCGGTAAGTGCTAAATCCTTCAAATCAGATCTCAA
GCAGTCTTCCCACTTCCGCCTTGGTCGTCCTCTCCTTCTGGAGCCGTCAACTGTAATCGACTCTA
CCATCTTGACCGCATCTGACGGTTGTCGCCTAAAGACATGCCCAAACCACCGTAGTCTTCTCTCC
CTCAATTTTTCGAATACAGGCACCACTCCCAAGGACTTCCTAATAGCAGAGTTTGGTGTCATGTC
TCACAGAGTCCTACCGCATGCCCATCGAAGCATTCT
Found at i:1543544 original size:2 final size:2
Alignment explanation
Indices: 1543537--1543574 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1543527 TATCTTAAGC
1543537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1543575 TTATTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1543638 original size:13 final size:14
Alignment explanation
Indices: 1543609--1543639 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1543599 TAAAATCCTA
1543609 TTTATAAATTTAAT
1 TTTATAAATTTAAT
1543623 TTTATAAA-TTAAT
1 TTTATAAATTTAAT
1543636 TTTA
1 TTTA
1543640 AGAAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTATAAATTTAAT
Found at i:1544431 original size:28 final size:27
Alignment explanation
Indices: 1544386--1544451 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
1544376 TTATTTAATT
* *
1544386 TATA-ATTATTTTCTTTCAAAATTTTTA
1 TATATATTATTAT-TTTCAAAATATTTA
*
1544413 TATATACTTATTATTTTCATAATATTTA
1 TATATA-TTATTATTTTCAAAATATTTA
1544441 TATATATTATT
1 TATATATTATT
1544452 TTTATTAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.26
28 19 0.56
29 6 0.18
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (27 bp):
TATATATTATTATTTTCAAAATATTTA
Found at i:1544447 original size:30 final size:30
Alignment explanation
Indices: 1544377--1544456 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
1544367 TATTCATATT
* *
1544377 TATTTA-ATTTATAATTATTTTCTTTCAAA
1 TATTTATATATATAATTATTATCTTTCAAA
* *
1544406 -ATTTTTATATATACTTATTAT-TTTCATAA
1 TATTTATATATATAATTATTATCTTTCA-AA
* *
1544435 TATTTATATATATTATTTTTAT
1 TATTTATATATATAATTATTAT
1544457 TAATGTTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
28 9 0.22
29 14 0.35
30 17 0.43
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (30 bp):
TATTTATATATATAATTATTATCTTTCAAA
Found at i:1550668 original size:21 final size:23
Alignment explanation
Indices: 1550635--1550697 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
1550625 ATTTTGGTGC
* *
1550635 AGAGGCAATCGATCCCCCCCATG-
1 AGAGG-AACCGATTCCCCCCATGA
**
1550658 AG-GGAACCGATTCCCCCTTTGA
1 AGAGGAACCGATTCCCCCCATGA
1550680 AGAGGAACCGATTCCCCC
1 AGAGGAACCGATTCCCCC
1550698 TACAGGGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 13 0.38
22 4 0.12
23 17 0.50
ACGTcount: A:0.25, C:0.37, G:0.22, T:0.16
Consensus pattern (23 bp):
AGAGGAACCGATTCCCCCCATGA
Found at i:1557132 original size:72 final size:72
Alignment explanation
Indices: 1557052--1557187 Score: 209
Period size: 72 Copynumber: 1.9 Consensus size: 72
1557042 ATACAATAAA
*
1557052 GCTTGAGTTATCCCCCGAAAACAATTGGTTAATAACCCCAGCTTTTTGGATAATATTAAGCTAAT
1 GCTTGAGTTATCCCCCGAAAACAATTGGTTAATAACCCCAGCTTTATGGATAATATTAAGCTAAT
1557117 TTGTTAT
66 TTGTTAT
* * ** * *
1557124 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATTGCCCCGGCTTTATGGATAATATTCAGCTAA
1 GCTTGAGTTATCCCCCGAAAACAATTGGTTAATAACCCCAGCTTTATGGATAATATTAAGCTAA
1557188 CCTATTATAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (72 bp):
GCTTGAGTTATCCCCCGAAAACAATTGGTTAATAACCCCAGCTTTATGGATAATATTAAGCTAAT
TTGTTAT
Found at i:1560021 original size:75 final size:75
Alignment explanation
Indices: 1559898--1560054 Score: 212
Period size: 75 Copynumber: 2.1 Consensus size: 75
1559888 GATAGAGCAC
*
1559898 GCTGAAAGCCCATTCCAATCATAATCAGGAATATTGAAACTTTTTGAACGTTTGTATTAGCCAAT
1 GCTGAAAGCCCATTCCAATCAGAATCAGGAATATTGAAACTTTTTGAACGTTTGTATTAGCCAAT
1559963 ACTGGGGCAT
66 ACTGGGGCAT
* * **
1559973 GCTGAAAGTCCC-TTTCAATCAGAATCAGGAATGTTG-ATGTATTTTGAACGTTTGTATTAGCCA
1 GCTGAAAG-CCCATTCCAATCAGAATCAGGAATATTGAAACT-TTTTGAACGTTTGTATTAGCCA
**
1560036 ATGTTGGGGCAT
64 ATACTGGGGCAT
1560048 GCT-AAAG
1 GCTGAAAG
1560055 ATCCATATCA
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
74 6 0.08
75 64 0.88
76 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (75 bp):
GCTGAAAGCCCATTCCAATCAGAATCAGGAATATTGAAACTTTTTGAACGTTTGTATTAGCCAAT
ACTGGGGCAT
Found at i:1560969 original size:54 final size:54
Alignment explanation
Indices: 1560911--1561063 Score: 198
Period size: 54 Copynumber: 2.8 Consensus size: 54
1560901 AATCTGTGCC
* * *
1560911 GAAGCCACATGAAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCTGGGAA
1 GAAGCCACATGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGAA
* * * *
1560965 GAAGCCACAGGAAAAAATAAATGTGTTGTCAAATGTTTTACGAACATCTGAGTA
1 GAAGCCACATGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGAA
** * * *
1561019 GAAATCACATGAGATGATGAATGTGTTGTCAAATTTTTTACGAAC
1 GAAGCCACATGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
1561064 CGGAAATTAT
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (54 bp):
GAAGCCACATGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGAA
Found at i:1562113 original size:45 final size:45
Alignment explanation
Indices: 1562049--1562566 Score: 865
Period size: 45 Copynumber: 11.5 Consensus size: 45
1562039 TTCCCACATA
*
1562049 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
1562094 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* *
1562139 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCATCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
1562184 AGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
1562229 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCTGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
1562274 TTTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* *
1562319 TGTAAGCCCTTTAGTGCATGATGTTTTCAAAACTTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
1562364 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1562409 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
1562454 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*** * *
1562499 TGTAATAACTTCAGTGCATGATGTTTTCAAAACCTTTGGGTCATT
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * *
1562544 TGTAAGACCTACAGTGCAAGATG
1 TGTAAGCCCTTCAGTGCATGATG
1562567 ATAAGACTTC
Statistics
Matches: 447, Mismatches: 26, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 447 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (45 bp):
TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
Found at i:1562126 original size:26 final size:26
Alignment explanation
Indices: 1562097--1562172 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 26
1562087 GGTCATCTGT
1562097 AAGCCCTTCAGTGCATGATGTTTTCA
1 AAGCCCTTCAGTGCATGATGTTTTCA
* *
1562123 AAG-CCTTC-GGGTCAT-CTG---T--
1 AAGCCCTTCAGTG-CATGATGTTTTCA
1562142 AAGCCCTTCAGTGCATGATGTTTTCA
1 AAGCCCTTCAGTGCATGATGTTTTCA
1562168 AAGCC
1 AAGCC
1562173 ATCGGGTCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 18
0.63 0.07 0.31
Matches are distributed among these distances:
19 3 0.08
20 8 0.22
21 5 0.14
24 5 0.14
25 8 0.22
26 8 0.22
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (26 bp):
AAGCCCTTCAGTGCATGATGTTTTCA
Found at i:1562751 original size:13 final size:13
Alignment explanation
Indices: 1562733--1562758 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1562723 TAAAATGATT
1562733 AAAATTATTATTA
1 AAAATTATTATTA
1562746 AAAATTATTATTA
1 AAAATTATTATTA
1562759 TTATGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATTATTATTA
Found at i:1562955 original size:19 final size:20
Alignment explanation
Indices: 1562916--1562956 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1562906 CCAAAACCTA
**
1562916 ATTAGGGTTTTCATATTTCT
1 ATTAGGGTTTTCATAACTCT
1562936 ATTAGGG-TTTCATAACTCT
1 ATTAGGGTTTTCATAACTCT
1562955 AT
1 AT
1562957 CCACGTCACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (20 bp):
ATTAGGGTTTTCATAACTCT
Found at i:1564188 original size:17 final size:17
Alignment explanation
Indices: 1564156--1564203 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
1564146 TAACAGTTTG
*
1564156 ATATTTTTCA-TTTAAT
1 ATATTTTGCATTTTAAT
1564172 ATATTTTGCATTTTAAT
1 ATATTTTGCATTTTAAT
*
1564189 AT-TATTGC-TTTTAAT
1 ATATTTTGCATTTTAAT
1564204 TTCTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.24
16 14 0.48
17 8 0.28
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.60
Consensus pattern (17 bp):
ATATTTTGCATTTTAAT
Found at i:1564225 original size:3 final size:3
Alignment explanation
Indices: 1564217--1564298 Score: 52
Period size: 3 Copynumber: 28.7 Consensus size: 3
1564207 TTTTATTTTG
* * *
1564217 ATT ATT ATT ATT -CT ATT TTT ATT GTT ATT -TT -TT ATAT ATGT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T ATT
*
1564260 A-A ATT ATT ATT -TT CATT ATT ATT -TT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT AT
1564299 CTTAAGTCAT
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
2 11 0.18
3 45 0.73
4 6 0.10
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1564244 original size:23 final size:21
Alignment explanation
Indices: 1564218--1564290 Score: 60
Period size: 23 Copynumber: 3.4 Consensus size: 21
1564208 TTTATTTTGA
1564218 TTATTATTATTCTATTTTTATT
1 TTATTATT-TTCTATTTTTATT
* **
1564240 GTTATT-TTTTATATATGTTTAAA
1 -TTATTATTTTCTAT-T-TTTATT
*
1564263 TTATTATTTTC-ATTATTATT
1 TTATTATTTTCTATTTTTATT
1564283 TTATTATT
1 TTATTATT
1564291 ATTATTATCT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
20 11 0.28
21 6 0.15
22 10 0.25
23 13 0.32
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (21 bp):
TTATTATTTTCTATTTTTATT
Found at i:1564279 original size:12 final size:11
Alignment explanation
Indices: 1564233--1564298 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 11
1564223 ATTATTCTAT
*
1564233 TTTTATTGTTA
1 TTTTATTATTA
1564244 TTTT-TTATATA
1 TTTTATTAT-TA
1564255 TGTTTAAATTATTA
1 T-TTT--ATTATTA
1564269 TTTTCATTATTA
1 TTTT-ATTATTA
1564281 TTTTATTATTA
1 TTTTATTATTA
1564292 TTATTAT
1 TT-TTAT
1564299 CTTAAGTCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
10 3 0.06
11 16 0.34
12 18 0.38
13 3 0.06
14 3 0.06
15 4 0.09
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:1564314 original size:2 final size:2
Alignment explanation
Indices: 1564307--1564332 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1564297 ATCTTAAGTC
1564307 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
1564333 TTATTTTTTA
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:1566561 original size:14 final size:15
Alignment explanation
Indices: 1566450--1566567 Score: 130
Period size: 15 Copynumber: 7.5 Consensus size: 15
1566440 TAATAAGGTT
1566450 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1566465 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1566480 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1566495 ATTTACTTTAAAATA
1 ATTTATTTTAAAATA
* *
1566510 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
1566529 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
1566547 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1566561 ATTTATT
1 ATTTATT
1566568 AGTATGAATT
Statistics
Matches: 88, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
14 12 0.14
15 56 0.64
16 4 0.05
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.05
22 6 0.07
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1566586 original size:32 final size:31
Alignment explanation
Indices: 1566547--1566644 Score: 115
Period size: 32 Copynumber: 3.4 Consensus size: 31
1566537 TTTTAAAATA
1566547 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATG-ATTG
1566579 ATTTATTTT--A-AA---A-TA-TA-GATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTG
1566601 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
1566633 ATTTATTTTAAA
1 ATTTATTTTAAA
1566645 ATATGGATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 13 0.23
23 1 0.02
24 3 0.05
25 4 0.07
26 1 0.02
28 1 0.02
29 4 0.07
30 3 0.05
32 26 0.46
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTAGTATGATTG
Found at i:1566604 original size:69 final size:67
Alignment explanation
Indices: 1566465--1566622 Score: 205
Period size: 69 Copynumber: 2.3 Consensus size: 67
1566455 TTTTAAAATA
*
1566465 ATTTATTTTAAAATAATTTATTATAAAATAATTTACTTTAAAATAAATTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTACTTTAAAATAAATTATTATAAAATATAGAT
1566530 TG
66 TG
* * * * *
1566532 ATTTATTTTAAAATAATTTATT-TTAAATAATTTA-TTAGTATGAATTGATTTATTTTAAAATAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTACTT--TA--AAATAAATTATTATAAAATAT
1566595 AGATTG
62 AGATTG
1566601 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
1566623 GTATGGATTG
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
65 2 0.03
66 11 0.14
67 24 0.30
68 12 0.15
69 31 0.39
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.51
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTACTTTAAAATAAATTATTATAAAATATAGAT
TG
Found at i:1566612 original size:54 final size:54
Alignment explanation
Indices: 1566547--1567203 Score: 272
Period size: 54 Copynumber: 12.1 Consensus size: 54
1566537 TTTTAAAATA
*
1566547 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
*
1566601 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
* * **
1566655 ATTTA--TT--AT--TGTAGTT-GTATGAATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAAT-ATAGATT-G
* * ** * * * *
1566704 TATGTA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT--AA-ATA-ATTT
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
* * * *
1566753 ATTAGTATGTATTAATTTATTT-TAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGG
1 ATT--TAT-T-TTAAATAATTTAT-TAGTATGGATTGATTTATTTT--A-AA---A-TA-TA--G
1566817 ATTG
51 ATTG
* *
1566821 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
* * *
1566875 ATTTA--TT--AT--TGTAGTT-GTATAGATTGATTTATTTTAAATAATTTATTAGTATGG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA--TA-TAG-ATTG
* * * *
1566929 ATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTTT--AA-ATA-ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
* * ** * * * * *
1566973 ATTAATATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTATTTTAAAATATAGATTG
* *
1567031 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT--AA-ATA-ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
* * * * * *** *
1567081 ATTT-GTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATAGATTG
*
1567143 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1567197 ATTTATT
1 ATTTATT
1567204 ATTGTAGTTG
Statistics
Matches: 459, Mismatches: 75, Indels: 138
0.68 0.11 0.21
Matches are distributed among these distances:
44 6 0.01
45 1 0.00
46 2 0.00
47 6 0.01
48 49 0.11
49 14 0.03
50 31 0.07
51 5 0.01
52 11 0.02
53 12 0.03
54 195 0.42
55 13 0.03
56 9 0.02
57 6 0.01
58 32 0.07
59 1 0.00
60 2 0.00
61 4 0.01
62 16 0.03
63 3 0.01
64 28 0.06
65 4 0.01
66 3 0.01
68 6 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
Found at i:1566638 original size:18 final size:18
Alignment explanation
Indices: 1566615--1566662 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1566605 ATTTTAAATA
*
1566615 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1566633 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1566655 ATTTATTA
1 ATTTATTA
1566663 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1566713 original size:32 final size:31
Alignment explanation
Indices: 1566671--1567106 Score: 211
Period size: 32 Copynumber: 14.7 Consensus size: 31
1566661 TATTGTAGTT
1566671 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATG-ATTGATTTATTTTAAATAATTTATTA
1566703 GTATGTATTGATTTATTTT-AA-AA--TA-T-
1 GTATG-ATTGATTTATTTTAAATAATTTATTA
1566729 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
*
1566757 GTATGTATTAATTTATTTT-AA-AA--TA-T-
1 GTATG-ATTGATTTATTTTAAATAATTTATTA
1566783 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
*
1566811 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
**
1566843 GTATGGATTGATTTATTTTAAA-ATATGGATT-
1 GTAT-GATTGATTTATTTTAAATA-ATTTATTA
* * *
1566874 G-ATTTATT-ATTGTAGTTGTATAGATTGATTTATT-
1 GTA-TGATTGATT-TA-TT-T-TA-AATAATTTATTA
* * * * * *
1566908 -T-TAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 GTATGATTGATTTATT--T-T-AAATAATTTA--TT--A
*
1566945 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
*
1566977 ATATGGATTGATTTATTTT-AA-AA--TA-T-
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
1567003 G-A--ATTGATTTATTTTAAA-A---TA-T-
1 GTATGATTGATTTATTTTAAATAATTTATTA
1567025 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
*
1567053 GTATAGATTGATTTATTTTAAATAATTTATTT
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
1567085 GTATAGATTGATTTATTTTAAA
1 GTAT-GATTGATTTATTTTAAA
1567107 ATATGGATTG
Statistics
Matches: 330, Mismatches: 22, Indels: 104
0.72 0.05 0.23
Matches are distributed among these distances:
22 58 0.18
23 10 0.03
24 4 0.01
25 1 0.00
26 8 0.02
27 6 0.02
28 9 0.03
29 3 0.01
30 12 0.04
31 14 0.04
32 170 0.52
33 5 0.02
34 10 0.03
36 7 0.02
37 1 0.00
38 2 0.01
39 1 0.00
40 9 0.03
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (31 bp):
GTATGATTGATTTATTTTAAATAATTTATTA
Found at i:1566720 original size:22 final size:22
Alignment explanation
Indices: 1566704--1566746 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1566694 AATTTATTAG
*
1566704 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1566726 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1566747 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1566778 original size:220 final size:218
Alignment explanation
Indices: 1566545--1567074 Score: 780
Period size: 220 Copynumber: 2.4 Consensus size: 218
1566535 TATTTTAAAA
*
1566545 TAATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTATTTT
1 TAATTTATTTTAAATAA-TTATTA-TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTT
1566610 AAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTAT
64 AAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTAT
*
1566675 -GAATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTGATTT
129 AG-ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTT
* *
1566739 ATTTTAAATAATTTATTAGTATGTAT
193 ATTTTAAATAATTTATTAATATGGAT
* * * * *
1566765 TAATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA
1 TAATTTATTTT-AAATA---ATT-A-TTATATGAATTGATTTATTTTAAAATATGGATTGATTTA
*
1566826 TTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTT
60 TTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTT
1566891 GTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
125 GTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1566956 TTTATTTTAAATAATTTATTAATATGGAT
190 TTTATTTTAAATAATTTATTAATATGGAT
*
1566985 TGATTTA-TTT---TAA--A--ATATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 TAATTTATTTTAAATAATTATTATATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
*
1567042 ATAATTTATTAGTATAGATTGATTTATTTTAAA
66 ATAATTTATTAGTATGGATTGATTTATTTTAAA
1567075 TAATTTATTT
Statistics
Matches: 281, Mismatches: 18, Indels: 32
0.85 0.05 0.10
Matches are distributed among these distances:
206 11 0.04
208 2 0.01
209 1 0.00
210 52 0.19
212 1 0.00
215 2 0.01
219 3 0.01
220 184 0.65
221 6 0.02
222 2 0.01
223 2 0.01
224 12 0.04
225 3 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (218 bp):
TAATTTATTTTAAATAATTATTATATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAG
ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
TTAAATAATTTATTAATATGGAT
Found at i:1566783 original size:22 final size:22
Alignment explanation
Indices: 1566758--1566800 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1566748 AATTTATTAG
*
1566758 TATGTATTAATTTATTTTAAAA
1 TATGGATTAATTTATTTTAAAA
*
1566780 TATGGATTGATTTATTTTAAA
1 TATGGATTAATTTATTTTAAA
1566801 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
TATGGATTAATTTATTTTAAAA
Found at i:1566930 original size:80 final size:80
Alignment explanation
Indices: 1566730--1567283 Score: 707
Period size: 80 Copynumber: 6.8 Consensus size: 80
1566720 TTAAAATATG
* *
1566730 GATTGATTTATTTTAAATAATTTATTAGTATGTATTAATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA-
* *
1566795 TTTAAATAATTTA-TTAGTATG
65 -TT--AT--TGTAGTT-GTATA
*
1566816 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1566881 TATTGTAGTTGTATA
66 TATTGTAGTTGTATA
1566896 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
* *
1566961 T-TTAAATAATT-TATTA
66 TATT--GTAGTTGTA-TA
* * * *
1566977 -ATATGGATTGA-TTT--AT--TTTA-AAATATGAATTGATTTATTTTAAAATATGGATTGATTT
1 GAT-T-GATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTT
*
1567035 ATTTTAAATAATTTA-TTAGTATA
64 A--TT--AT--TGTAGTT-GTATA
* *
1567058 GATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
*
1567123 TATTGTAGTTGTATG
66 TATTGTAGTTGTATA
1567138 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
*
1567203 TATTGTAGTTGTATG
66 TATTGTAGTTGTATA
*
1567218 GATTGATTTATTTTAAATAATTAATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1567283 T
66 T
1567284 TTAAATAATT
Statistics
Matches: 421, Mismatches: 24, Indels: 52
0.85 0.05 0.10
Matches are distributed among these distances:
76 36 0.09
77 4 0.01
78 2 0.00
79 4 0.01
80 233 0.55
81 23 0.05
82 13 0.03
83 3 0.01
84 4 0.01
85 4 0.01
86 95 0.23
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (80 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
TATTGTAGTTGTATA
Found at i:1566949 original size:22 final size:22
Alignment explanation
Indices: 1566924--1567042 Score: 112
Period size: 22 Copynumber: 5.0 Consensus size: 22
1566914 AATTTATTAG
1566924 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1566946 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
** *
1566970 TTTATTAATATGGATTGATTTATTTTAAAA
1 --TATGGAT-T-GATTTA-TT---TTAAAA
*
1567000 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1567022 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1567043 TAATTTATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
22 44 0.54
23 2 0.02
24 2 0.02
25 2 0.02
26 10 0.12
27 2 0.02
28 11 0.14
29 2 0.02
30 2 0.02
31 2 0.02
32 2 0.02
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1567015 original size:242 final size:239
Alignment explanation
Indices: 1566725--1567298 Score: 877
Period size: 242 Copynumber: 2.3 Consensus size: 239
1566715 TTATTTTAAA
*
1566725 ATATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTAATTTATTTTAAAATATGGATTGA
1 ATATGGATTGATTTATTTTAAATAA-TTA-T-G-A---ATTGATTTATTTTAAAATATGGATTGA
* *
1566790 TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGAT
59 TTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATAGATTGAT
1566855 TTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTA
124 TTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTA
*
1566920 TTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TT
189 TTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT
1566976 AATATGGATTGATTTATTTT-AA-AA-TATGAATTGATTTATTTTAAAATATGGATTGATTTATT
1 -ATATGGATTGATTTATTTTAAATAATTATGAATTGATTTATTTTAAAATATGGATTGATTTATT
1567038 TTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTT
65 TTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTT
*
1567103 TAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTA
130 TAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTA
1567168 TGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTT
195 TGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTT
*
1567213 GTATGGATTGATTTATTTTAAATAATTAATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 ATATGGATTGATTTATTTTAAATAATT-A-T-G-A---ATTGATTTATTTTAAAATATGGATTGA
1567278 TTTATTTTAAATAATTTATTA
59 TTTATTTTAAATAATTTATTA
1567299 TTGTAGTTGT
Statistics
Matches: 305, Mismatches: 6, Indels: 28
0.90 0.02 0.08
Matches are distributed among these distances:
236 21 0.07
237 4 0.01
238 4 0.01
239 1 0.00
240 3 0.01
241 1 0.00
242 194 0.64
243 1 0.00
245 1 0.00
246 49 0.16
247 1 0.00
248 2 0.01
250 2 0.01
251 2 0.01
252 19 0.06
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (239 bp):
ATATGGATTGATTTATTTTAAATAATTATGAATTGATTTATTTTAAAATATGGATTGATTTATTT
TAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTT
AAAATATGGATTGATTTATTATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTAT
GGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTT
Found at i:1567068 original size:18 final size:17
Alignment explanation
Indices: 1567045--1567101 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
1567035 ATTTTAAATA
1567045 ATTTATTAGTATAGATTG
1 ATTTATT-GTATAGATTG
* *
1567063 ATTTATT-T-TA-AATA
1 ATTTATTGTATAGATTG
1567077 ATTTATTTGTATAGATTG
1 ATTTA-TTGTATAGATTG
1567095 ATTTATT
1 ATTTATT
1567102 TTAAAATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
16 2 0.06
17 4 0.13
18 14 0.45
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (17 bp):
ATTTATTGTATAGATTG
Found at i:1567102 original size:18 final size:16
Alignment explanation
Indices: 1567026--1567105 Score: 69
Period size: 14 Copynumber: 5.0 Consensus size: 16
1567016 TTAAAATATG
1567026 GATTGATTTATTTTAA
1 GATTGATTTATTTTAA
* *
1567042 -A-TAATTTATTAGTATA
1 GATTGATTTATT-TTA-A
1567058 GATTGATTTATTTTAA
1 GATTGATTTATTTTAA
*
1567074 -A-TAATTTATTTGTATA
1 GATTGATTTATTT-TA-A
1567090 GATTGATTTATTTTAA
1 GATTGATTTATTTTAA
1567106 AATATGGATT
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
14 17 0.34
15 6 0.12
16 4 0.08
17 6 0.12
18 17 0.34
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
GATTGATTTATTTTAA
Found at i:1567180 original size:18 final size:18
Alignment explanation
Indices: 1567157--1567204 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1567147 ATTTTAAATA
*
1567157 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1567175 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1567197 ATTTATTA
1 ATTTATTA
1567205 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1567271 original size:22 final size:22
Alignment explanation
Indices: 1567246--1567288 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1567236 AATTAATTAG
1567246 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1567268 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1567289 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1567285 original size:54 final size:54
Alignment explanation
Indices: 1566672--1567298 Score: 550
Period size: 54 Copynumber: 11.6 Consensus size: 54
1566662 ATTGTAGTTG
* *
1566672 TATGAATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
1566726 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTAATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1566780 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * ** * * * ***
1566833 TA---ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAA
*
1566892 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
1566946 TATGGATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* ** ** * ** * * *
1567000 TATGAATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
* * *
1567054 TATAGATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
1567108 TATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAA
** ** * ** * * * ***
1567155 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGTTG
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAA
*
1567214 TATGGATTGATTTATTTTAAATAATTAATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1567268 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
1567299 TTGTAGTTGT
Statistics
Matches: 456, Mismatches: 82, Indels: 70
0.75 0.13 0.12
Matches are distributed among these distances:
47 4 0.01
48 26 0.06
49 3 0.01
50 21 0.05
51 1 0.00
52 7 0.02
53 16 0.04
54 275 0.60
55 20 0.04
56 14 0.03
57 13 0.03
58 35 0.08
59 3 0.01
60 2 0.00
62 16 0.04
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:1567348 original size:31 final size:31
Alignment explanation
Indices: 1567313--1567371 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1567303 AGTTGTATGG
*
1567313 ATTATTTAAAT-TTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTT-AGTATTGCAAAACTAAA
1567344 ATTATTTAAATCTTAGTATTGCAAAACT
1 ATTATTTAAATCTTAGTATTGCAAAACT
1567372 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTTAGTATTGCAAAACTAAA
Found at i:1571195 original size:54 final size:54
Alignment explanation
Indices: 1571052--1571445 Score: 315
Period size: 55 Copynumber: 7.2 Consensus size: 54
1571042 TGAAAAATCT
* * *
1571052 TCGAACAATCTTCAGCAAACGGGTCCTCTCCCTATTCCTTCAGGGAGTATAAGAC
1 TCGAACAATCTTCAGCAAACGAGT-TTCTCCCTATTCCTTCAGGGAGTATAAGAA
* * * * *
1571107 TCGAATAATCTTCAACAAAC-ATGTCTTCTTCCTATTCCTCCAGAGAGTATAAGAA
1 TCGAACAATCTTCAGCAAACGA-GT-TTCTCCCTATTCCTTCAGGGAGTATAAGAA
* *
1571162 TC-AACAATCTTCAGCAAACGAGTTTGCTCCCTATTCCTTTAGGGAGTATAAGAT
1 TCGAACAATCTTCAGCAAACGAGTTT-CTCCCTATTCCTTCAGGGAGTATAAGAA
** * *
1571216 TTAAACAATTTTCAGCAAAC-AGTTCTCTCCCTATT-CTTCCAGCGAGTAT-AGAA
1 TCGAACAATCTTCAGCAAACGAGTT-TCTCCCTATTCCTT-CAGGGAGTATAAGAA
* * *
1571269 CTCGAACAATCTTCTG-ACAACGGGTTTGCTCCCTATTCTTTCAGGGAGTAT-AGAA
1 -TCGAACAATCTTCAGCA-AACGAGTTT-CTCCCTATTCCTTCAGGGAGTATAAGAA
* * * * * *
1571324 CTCGAACAATCTTCTG-ACAACGGGTTCGCTCCCTATTCTTTTAGGCAGTAT-AGAA
1 -TCGAACAATCTTCAGCA-AACGAGTT-TCTCCCTATTCCTTCAGGGAGTATAAGAA
** * * *
1571379 CTCGAACAATCTTTTG-ACAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAA-AA
1 -TCGAACAATCTTCAGCA-AACGAGTT-TCTCCCTATTCCTTCAGGGAGTATAAGAA
1571434 CTCGAACAATCT
1 -TCGAACAATCT
1571446 CGTTTTGCTC
Statistics
Matches: 293, Mismatches: 33, Indels: 26
0.83 0.09 0.07
Matches are distributed among these distances:
53 9 0.03
54 77 0.26
55 204 0.70
56 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (54 bp):
TCGAACAATCTTCAGCAAACGAGTTTCTCCCTATTCCTTCAGGGAGTATAAGAA
Found at i:1571277 original size:109 final size:108
Alignment explanation
Indices: 1571052--1571445 Score: 419
Period size: 109 Copynumber: 3.6 Consensus size: 108
1571042 TGAAAAATCT
* * *
1571052 TCGAACAATCTTCAG-CAAACGGGTCCT-CTCCCTATTCCTTCAGGGAGTATAAGACTCGAATAA
1 TCGAACAATCTTCAGAC-AACGGGT-TTGCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAA
* * *
1571115 TCTTCAACAAACA-TGTCTTCTTCCTATTCCTCCAGAGAGTATAAGAA-
64 TCTTCAGCAAACAGT-TC-TCTCCCTATTCTTCCAG-GAGTAT-AGAAC
* * **
1571162 TC-AACAATCTTCAG-CAAACGAGTTTGCTCCCTATTCCTTT-AGGGAGTATAAGATTTAAACAA
1 TCGAACAATCTTCAGAC-AACGGGTTTGCTCCCTATT-CTTTCAGGGAGTATAAGACTCGAACAA
*
1571224 TTTTCAGCAAACAGTTCTCTCCCTATTCTTCCAGCGAGTATAGAAC
64 TCTTCAGCAAACAGTTCTCTCCCTATTCTTCCAG-GAGTATAGAAC
*
1571270 TCGAACAATCTTCTGACAACGGGTTTGCTCCCTATTCTTTCAGGGAGTAT-AGAACTCGAACAAT
1 TCGAACAATCTTCAGACAACGGGTTTGCTCCCTATTCTTTCAGGGAGTATAAG-ACTCGAACAAT
* * * **
1571334 CTTCTG-ACAACGGGTTCGCTCCCTATTCTTTTAGGCAGTATAGAAC
65 CTTCAGCA-AAC-AGTTCTCTCCCTATTCTTCCAGG-AGTATAGAAC
** * *
1571380 TCGAACAATCTTTTGACAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAAAACTCGAACAATC
1 TCGAACAATCTTCAGACAACGGGTTTGCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATC
1571445 T
66 T
1571446 CGTTTTGCTC
Statistics
Matches: 246, Mismatches: 26, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
107 4 0.02
108 31 0.13
109 114 0.46
110 96 0.39
111 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (108 bp):
TCGAACAATCTTCAGACAACGGGTTTGCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATC
TTCAGCAAACAGTTCTCTCCCTATTCTTCCAGGAGTATAGAAC
Found at i:1572799 original size:7 final size:7
Alignment explanation
Indices: 1572763--1572859 Score: 59
Period size: 7 Copynumber: 14.6 Consensus size: 7
1572753 TTTTCTTTTC
1572763 TTTTCAT
1 TTTTCAT
1572770 TTTTC--
1 TTTTCAT
1572775 TTTTC-T
1 TTTTCAT
*
1572781 TCTTCTAT
1 TTTTC-AT
1572789 TTTTCAT
1 TTTTCAT
1572796 TTTTCATT
1 TTTTCA-T
*
1572804 TTTTCTCT
1 TTTTC-AT
1572812 TTTTCAT
1 TTTTCAT
1572819 TTTTC-T
1 TTTTCAT
* *
1572825 CTTTCTT
1 TTTTCAT
1572832 TCTTTC--
1 T-TTTCAT
1572838 TTTTCA-
1 TTTTCAT
1572844 TTTTC--
1 TTTTCAT
1572849 TTTTCAT
1 TTTTCAT
1572856 TTTT
1 TTTT
1572860 TAATTTTTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
5 14 0.19
6 15 0.20
7 24 0.32
8 21 0.28
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTCAT
Found at i:1572799 original size:8 final size:8
Alignment explanation
Indices: 1572788--1572935 Score: 72
Period size: 8 Copynumber: 17.2 Consensus size: 8
1572778 TCTTCTTCTA
1572788 TTTTTCA-
1 TTTTTCAT
1572795 TTTTTCAT
1 TTTTTCAT
1572803 TTTTTC-T
1 TTTTTCAT
1572810 CTTTTTCAT
1 -TTTTTCAT
1572819 TTTTCTC-T
1 TTTT-TCAT
*
1572827 TTCTTTCTT
1 TT-TTTCAT
1572836 TCTTTTCATTT
1 T-TTTTCA--T
1572847 TCTTTTCAT
1 T-TTTTCAT
*
1572856 TTTTTAATTT
1 TTTTTCA--T
*
1572866 TTTTTAATT
1 TTTTTCA-T
*
1572875 TTTTTAAT
1 TTTTTCAT
*
1572883 TTTTTCCCT
1 TTTTT-CAT
1572892 TTTTCATCAT
1 TTTT--TCAT
1572902 TTTTT-ATT
1 TTTTTCA-T
*
1572910 TTTCTTCTT
1 TTT-TTCAT
1572919 TTTTTC-T
1 TTTTTCAT
1572926 TTTTTCAT
1 TTTTTCAT
1572934 TT
1 TT
1572936 CTTTTTCAAG
Statistics
Matches: 117, Mismatches: 6, Indels: 35
0.74 0.04 0.22
Matches are distributed among these distances:
7 16 0.14
8 43 0.37
9 33 0.28
10 15 0.13
11 10 0.09
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTCAT
Found at i:1572800 original size:43 final size:44
Alignment explanation
Indices: 1572753--1572859 Score: 120
Period size: 44 Copynumber: 2.5 Consensus size: 44
1572743 CCTCCTTTTA
1572753 TTTTC-TTTTCTTTTCATTTTTC--TTTTCT-TCTTCTATT-TTTC
1 TTTTCATTTTCTTTTCATTTTTCATTTTTCTCT-TTCT-TTCTTTC
*
1572794 ATTTTTCATTTT-TTCTC-TTTTTCATTTTTCTCTTTCTTTCTTTC
1 --TTTTCATTTTCTTTTCATTTTTCATTTTTCTCTTTCTTTCTTTC
1572838 TTTTCATTTTCTTTTCATTTTT
1 TTTTCATTTTCTTTTCATTTTT
1572860 TAATTTTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
42 16 0.29
43 15 0.27
44 23 0.42
45 1 0.02
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.75
Consensus pattern (44 bp):
TTTTCATTTTCTTTTCATTTTTCATTTTTCTCTTTCTTTCTTTC
Found at i:1572814 original size:16 final size:15
Alignment explanation
Indices: 1572763--1572828 Score: 62
Period size: 15 Copynumber: 4.1 Consensus size: 15
1572753 TTTTCTTTTC
1572763 TTTTCATTTTTCTTTTCT
1 TTTTCATTTTTC---TCT
* *
1572781 TCTTCTATTTTTC-AT
1 TTTTC-ATTTTTCTCT
1572796 TTTTCATTTTTTCTCT
1 TTTTCA-TTTTTCTCT
1572812 TTTTCATTTTTCTCT
1 TTTTCATTTTTCTCT
1572827 TT
1 TT
1572829 CTTTCTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 1 0.02
15 22 0.54
16 7 0.17
18 4 0.10
19 7 0.17
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCATTTTTCTCT
Found at i:1572850 original size:15 final size:15
Alignment explanation
Indices: 1572747--1572851 Score: 64
Period size: 16 Copynumber: 7.0 Consensus size: 15
1572737 TTGAGACCTC
1572747 CTTTT-ATTTTCTTTT
1 CTTTTCATTTTC-TTT
1572762 CTTTTCATTTTTCTTTT
1 CTTTTCA-TTTTC-TTT
*
1572779 CTTCTTC-TATT-TTT
1 CTT-TTCATTTTCTTT
1572793 CATTTTTCATTTT-TTCT
1 C--TTTTCATTTTCTT-T
*
1572810 CTTTTTCATTTT-TCT
1 C-TTTTCATTTTCTTT
1572825 C-TTTC--TTTCTTT
1 CTTTTCATTTTCTTT
1572837 CTTTTCATTTTCTTT
1 CTTTTCATTTTCTTT
1572852 TCATTTTTTA
Statistics
Matches: 75, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
11 3 0.04
12 3 0.04
13 8 0.11
14 4 0.05
15 17 0.23
16 23 0.31
17 14 0.19
18 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTTCATTTTCTTT
Found at i:1572869 original size:9 final size:9
Alignment explanation
Indices: 1572855--1572887 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
1572845 TTTCTTTTCA
1572855 TTTTTTAATT
1 TTTTTTAA-T
1572865 TTTTTTAAT
1 TTTTTTAAT
1572874 TTTTTTAAT
1 TTTTTTAAT
1572883 TTTTT
1 TTTTT
1572888 CCCTTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:1572870 original size:10 final size:10
Alignment explanation
Indices: 1572855--1572887 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
1572845 TTTCTTTTCA
1572855 TTTTTTAATT
1 TTTTTTAATT
1572865 TTTTTTAA-T
1 TTTTTTAATT
1572874 TTTTTTAATT
1 TTTTTTAATT
1572884 TTTT
1 TTTT
1572888 CCCTTTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:1572911 original size:17 final size:17
Alignment explanation
Indices: 1572891--1572929 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1572881 ATTTTTTCCC
1572891 TTTTTCATCATTTTTTA
1 TTTTTCATCATTTTTTA
* * *
1572908 TTTTTCTTCTTTTTTTC
1 TTTTTCATCATTTTTTA
1572925 TTTTT
1 TTTTT
1572930 TCATTTCTTT
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:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCATCATTTTTTA
Found at i:1572940 original size:17 final size:16
Alignment explanation
Indices: 1572769--1572940 Score: 65
Period size: 19 Copynumber: 10.3 Consensus size: 16
1572759 TTTCTTTTCA
*
1572769 TTTTTCTTTTCTTCTTCT
1 TTTTTCTTTT-TTCAT-T
*
1572787 ATTTTTCATTTTTCA-T
1 -TTTTTCTTTTTTCATT
1572803 TTTTTCTCTTTTTCA--
1 TTTTTCT-TTTTTCATT
*
1572818 TTTTTC-TCTTTC-TT
1 TTTTTCTTTTTTCATT
*
1572832 TCTTTC--TTTTCATTT
1 TTTTTCTTTTTTCA-TT
*
1572847 TCTTTTCATTTTTTAATTT
1 T-TTTTC-TTTTTTCA-TT
* *
1572866 TTTTTAATTTTTTTAATT
1 TTTTT--CTTTTTTCATT
*
1572884 TTTTCCCTTTTTCATCATT
1 TTTT-TCTTTTT--TCATT
1572903 TTTTAT-TTTTCTTC-TT
1 TTTT-TCTTTT-TTCATT
1572919 TTTTTCTTTTTTCATT
1 TTTTTCTTTTTTCATT
1572935 TCTTTT
1 T-TTTT
1572941 TCAAGTGAAA
Statistics
Matches: 121, Mismatches: 14, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
13 9 0.07
14 5 0.04
15 19 0.16
16 25 0.21
17 11 0.09
18 17 0.14
19 35 0.29
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTCTTTTTTCATT
Found at i:1579420 original size:45 final size:46
Alignment explanation
Indices: 1579365--1579452 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
1579355 CATTAAAAAC
1579365 CCTAACCGCATGATATCTAATTCGCATGC-TTATTCGAAAAATAAA
1 CCTAACCGCATGATATCTAATTCGCATGCATTATTCGAAAAATAAA
* *
1579410 CCTAACCGCATGATATCTAGTTCGTATGCATTTATTCGAAAAA
1 CCTAACCGCATGATATCTAATTCGCATGCA-TTATTCGAAAAA
1579453 CGAAAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 27 0.69
47 12 0.31
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (46 bp):
CCTAACCGCATGATATCTAATTCGCATGCATTATTCGAAAAATAAA
Found at i:1581750 original size:20 final size:22
Alignment explanation
Indices: 1581705--1581762 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1581695 GCATGGGTAG
1581705 TGCATCGATGCACATGTTTAAGAA
1 TGCATCGATGCAC-TG-TTAAGAA
1581729 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
1581749 TGCATCTATGCACT
1 TGCATCGATGCACT
1581763 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
21 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1582565 original size:18 final size:18
Alignment explanation
Indices: 1582542--1582683 Score: 239
Period size: 18 Copynumber: 7.9 Consensus size: 18
1582532 AAGGGTCTAT
1582542 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
1582560 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
1582578 GTGGGCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
1582596 GTGGTCCTTCGAGACATA
1 GTGGTCCTTCGGGACATA
1582614 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
1582632 ATGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
1582650 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
1582668 GTTGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
1582684 AATTCTACGC
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 116 1.00
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.27
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:1589186 original size:20 final size:19
Alignment explanation
Indices: 1589149--1589187 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1589139 TTCAAGCATG
* *
1589149 GAAAACATGAACATATGGT
1 GAAAACATCAACAAATGGT
1589168 GAAAATCATCAACAAATGGT
1 GAAAA-CATCAACAAATGGT
1589188 ACCAAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.21
Consensus pattern (19 bp):
GAAAACATCAACAAATGGT
Found at i:1589579 original size:230 final size:228
Alignment explanation
Indices: 1589169--1589604 Score: 678
Period size: 230 Copynumber: 1.9 Consensus size: 228
1589159 ACATATGGTG
* * *
1589169 AAAATCATCAACAAATGGTACCAAATGATAGAGAATTTAATGTAGAATAATTTTGTATTTCATGC
1 AAAAGCATCAACAAATGGTACAAAATGATAGAGAATTTAATGCAGAATAATTTTGTATTTCATGC
*
1589234 TTTCATCCAAAATCCAAATAAATTGGCTTGAAAATCAAAAGAAAATTAATTCTTCTTACCTTAGG
66 TTTCATCCAAAATCCAAATAAATTGGCTTGAAAAACAAAAGAAAATTAATTCTTCTTACCTTAGG
*
1589299 GGTTCACGGCTTGGAGGAGGAAACATGGACAAATTTCATGAAAATTTTAATAAAATA-CAAAGTT
131 GGTTCACGGCTTGGAGGAGAAAACATGGACAAATTTCATGAAAATTTTAATAAAATATC-AAGTT
1589363 CACTTGTCTTTTATTTAATTAAAATGAATTAGAA
195 CACTTGTCTTTTATTTAATTAAAATGAATTAGAA
* *
1589397 AAAAGCATGAACAAATGGTACAAAATGATAGAGAATTTCATGCAGAATAATTTTGTATTTCA-GC
1 AAAAGCATCAACAAATGGTACAAAATGATAGAGAATTTAATGCAGAATAATTTTGTATTTCATGC
* * * ** *
1589461 TTTCATCCAACATCCAAATAAATTGGCTTGAAAAAAAGAATAAGAAATTTTCTTCTTTTTACCTT
66 TTTCATCCAAAATCCAAATAAATTGGCTTG--AAAAACAA-AAGAAAATTAATTCTTCTTACCTT
*
1589526 AGGGGTTCACGGCTTGGAGGAGAAAACATGGACAAGTTTCATGAAAATTTTAATAAAATATCAAG
128 AGGGGTTCACGGCTTGGAGGAGAAAACATGGACAAATTTCATGAAAATTTTAATAAAATATCAAG
* *
1589591 TTCATTTTTCTTTT
193 TTCACTTGTCTTTT
1589605 GAAATCTCTT
Statistics
Matches: 188, Mismatches: 16, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
227 31 0.16
228 57 0.30
229 6 0.03
230 93 0.49
231 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (228 bp):
AAAAGCATCAACAAATGGTACAAAATGATAGAGAATTTAATGCAGAATAATTTTGTATTTCATGC
TTTCATCCAAAATCCAAATAAATTGGCTTGAAAAACAAAAGAAAATTAATTCTTCTTACCTTAGG
GGTTCACGGCTTGGAGGAGAAAACATGGACAAATTTCATGAAAATTTTAATAAAATATCAAGTTC
ACTTGTCTTTTATTTAATTAAAATGAATTAGAA
Found at i:1593456 original size:22 final size:22
Alignment explanation
Indices: 1593431--1593472 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1593421 TCCTAATTTT
1593431 AATTTAATTTAATAAA-ATATTG
1 AATTTAATTTAA-AAATATATTG
1593453 AATTTAATTTAAAAATATAT
1 AATTTAATTTAAAAATATAT
1593473 AAATAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AATTTAATTTAAAAATATATTG
Found at i:1597321 original size:29 final size:29
Alignment explanation
Indices: 1597287--1597346 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1597277 CCTAAATTAA
*
1597287 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTAATTGCTTACATCAATTTAGT
1597316 TTTGATGTAATTGCTTACATCAATTTAGT
1 TTTGATGTAATTGCTTACATCAATTTAGT
1597345 TT
1 TT
1597347 GGTGAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.50
Consensus pattern (29 bp):
TTTGATGTAATTGCTTACATCAATTTAGT
Found at i:1601963 original size:29 final size:29
Alignment explanation
Indices: 1601929--1601987 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1601919 CCTAAATTAA
*
1601929 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
1601958 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
1601987 T
1 T
1601988 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Found at i:1608696 original size:65 final size:64
Alignment explanation
Indices: 1608561--1608716 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 64
1608551 ACACCCCATT
1608561 TCGAATGCATTTTATGCATCGATGCACTACCATACATCGATGCACTCAGGATTTTATGGAAACA
1 TCGAATGCATTTTATGCATCGATGCACTACCATACATCGATGCACTCAGGATTTTATGGAAACA
* * * * *
1608625 TAGAATGCGTTTTATCCATCGATGCAC-AGTCCATGCATCGATGCACTCCAGGCTTGTT-T-GAA
1 TCGAATGCATTTTATGCATCGATGCACTA--CCATACATCGATGCACT-CAGGATT-TTATGGAA
1608687 ACA
62 ACA
*
1608690 TCGAATGCATTTTATGCATCTATGCAC
1 TCGAATGCATTTTATGCATCGATGCAC
1608717 CCTTAGTGCA
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 24 0.30
65 45 0.57
66 7 0.09
67 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (64 bp):
TCGAATGCATTTTATGCATCGATGCACTACCATACATCGATGCACTCAGGATTTTATGGAAACA
Found at i:1614358 original size:21 final size:21
Alignment explanation
Indices: 1614334--1614455 Score: 77
Period size: 21 Copynumber: 5.6 Consensus size: 21
1614324 TTATGCATAA
1614334 TGCATCGATACACTATGAAGG
1 TGCATCGATACACTATGAAGG
* *
1614355 TGCATCGATGCATCCCTATGAATG
1 TGCATCGAT--A-CACTATGAAGG
* * *
1614379 TGCAACGATACACCATGAAGA
1 TGCATCGATACACTATGAAGG
* * * *
1614400 TGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACT--ATGAAGG
* *
1614423 TGCATCGATGCACTCA-GCA-G
1 TGCATCGATACACT-ATGAAGG
1614443 TGCATCGATACAC
1 TGCATCGATACAC
1614456 CCATCAGAGT
Statistics
Matches: 79, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
20 13 0.16
21 29 0.37
22 2 0.03
23 18 0.23
24 17 0.22
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (21 bp):
TGCATCGATACACTATGAAGG
Found at i:1614409 original size:45 final size:44
Alignment explanation
Indices: 1614334--1614431 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 44
1614324 TTATGCATAA
* * *
1614334 TGCATCGATACACTATGAAGGTGCATCGATGCA-TCCCTATGAATG
1 TGCATCGATACACCATGAAGATGCACCGATGCACT-CCT-TGAATG
*
1614379 TGCAACGATACACCATGAAGATGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACCATGAAGATGCACCGATGCACTCCTTGAATG
1614423 TGCATCGAT
1 TGCATCGAT
1614432 GCACTCAGCA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
44 14 0.30
45 32 0.68
46 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (44 bp):
TGCATCGATACACCATGAAGATGCACCGATGCACTCCTTGAATG
Found at i:1614426 original size:23 final size:23
Alignment explanation
Indices: 1614349--1614437 Score: 78
Period size: 23 Copynumber: 3.9 Consensus size: 23
1614339 CGATACACTA
*
1614349 TGAAGGTGCATCGATGCA-TCCCT
1 TGAATGTGCATCGATGCACT-CCT
* * *
1614372 ATGAATGTGCAACGAT--ACACCA
1 -TGAATGTGCATCGATGCACTCCT
*
1614394 TGAA-GATGCACCGATGCACTCCT
1 TGAATG-TGCATCGATGCACTCCT
1614417 TGAATGTGCATCGATGCACTC
1 TGAATGTGCATCGATGCACTC
1614438 AGCAGTGCAT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 12 0.23
22 3 0.06
23 22 0.42
24 14 0.27
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (23 bp):
TGAATGTGCATCGATGCACTCCT
Found at i:1614848 original size:18 final size:19
Alignment explanation
Indices: 1614808--1614847 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1614798 TAATTTCATC
*
1614808 AAAA-ACAAACAATTTTCA
1 AAAATACAAAAAATTTTCA
*
1614826 AAAATACAAAAAATTTTGA
1 AAAATACAAAAAATTTTCA
1614845 AAA
1 AAA
1614848 TCATTGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.65, C:0.10, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAATACAAAAAATTTTCA
Found at i:1616432 original size:27 final size:27
Alignment explanation
Indices: 1616400--1616456 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1616390 CTTTGAATGC
* *
1616400 TTGAACTTATAATT-ATTTATTTGGTTT
1 TTGAACTTAT-ATTGATTTATTAGATTT
1616427 TTGAACTTATATTGATTTATTAGATTT
1 TTGAACTTATATTGATTTATTAGATTT
1616454 TTG
1 TTG
1616457 CATCATTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.26, C:0.04, G:0.12, T:0.58
Consensus pattern (27 bp):
TTGAACTTATATTGATTTATTAGATTT
Found at i:1617145 original size:65 final size:65
Alignment explanation
Indices: 1617069--1617193 Score: 191
Period size: 65 Copynumber: 1.9 Consensus size: 65
1617059 AATGCATTTT
1617069 ATGCATCGATGCACT-CAGGATT-TTATAGAAACATCGAATGCATTTTATGCATCGATGCACAGA
1 ATGCATCGATGCACTCCAGGATTGTT-T-GAAACATCGAATGCATTTTATGCATCGATGCACAGA
1617132 CC
64 CC
* * *
1617134 ATGCATCGATGCATTCCAGGCTTGTTTGAAACATCGAATGTATTTTATGCATCGATGCAC
1 ATGCATCGATGCACTCCAGGATTGTTTGAAACATCGAATGCATTTTATGCATCGATGCAC
1617194 CCTTAGTGCA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
65 46 0.84
66 7 0.13
67 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (65 bp):
ATGCATCGATGCACTCCAGGATTGTTTGAAACATCGAATGCATTTTATGCATCGATGCACAGACC
Found at i:1625102 original size:27 final size:26
Alignment explanation
Indices: 1625072--1625129 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
1625062 TTTAGTAAAA
* *
1625072 TTTTAAAATTTAATTTTTTATCATTAT
1 TTTTAAAATTTAATATATTAT-ATTAT
* *
1625099 TTTTAAATTTTTATATATTATATTAT
1 TTTTAAAATTTAATATATTATATTAT
1625125 TTTTA
1 TTTTA
1625130 TGGTGGTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTTAAAATTTAATATATTATATTAT
Found at i:1625979 original size:15 final size:16
Alignment explanation
Indices: 1625956--1625989 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1625946 ATTAGGGTTT
*
1625956 TTAATTATGAA-TTAA
1 TTAAATATGAATTTAA
1625971 TTAAATATGAATTTAA
1 TTAAATATGAATTTAA
1625987 TTA
1 TTA
1625990 TTCTGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TTAAATATGAATTTAA
Found at i:1627945 original size:17 final size:16
Alignment explanation
Indices: 1627923--1627956 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1627913 TAAAAACAGT
1627923 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1627940 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1627956 A
1 A
1627957 TCCTCACGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1638085 original size:17 final size:16
Alignment explanation
Indices: 1638063--1638096 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1638053 TAAAAACAGT
1638063 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1638080 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1638096 A
1 A
1638097 TCTTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1646255 original size:24 final size:24
Alignment explanation
Indices: 1646223--1646287 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
1646213 TCTAGATCAT
*
1646223 GAGTCAACTCAGACCGAGTTAGCC
1 GAGTCAACTCAGACCGAGTAAGCC
* *
1646247 GAGTCAACTTAGACCGGGTAAGCC
1 GAGTCAACTCAGACCGAGTAAGCC
* *
1646271 GAGTCAAATCATACCGA
1 GAGTCAACTCAGACCGA
1646288 ATATGTTAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (24 bp):
GAGTCAACTCAGACCGAGTAAGCC
Found at i:1649492 original size:86 final size:86
Alignment explanation
Indices: 1649345--1649517 Score: 319
Period size: 86 Copynumber: 2.0 Consensus size: 86
1649335 TCCAGAAATT
* * *
1649345 AATGGAGTTGCCCTTGCCAACGACACATTCCACCTCAAGAGTGAACAAATCATATGGATCGTTAA
1 AATGGAGTTGCCCTTGCCAACGACACATCCCACCTCAAGAGTGAACAAATCACATGAATCGTTAA
1649410 ACGGACTTGTTAACAAATAAA
66 ACGGACTTGTTAACAAATAAA
1649431 AATGGAGTTGCCCTTGCCAACGACACATCCCACCTCAAGAGTGAACAAATCACATGAATCGTTAA
1 AATGGAGTTGCCCTTGCCAACGACACATCCCACCTCAAGAGTGAACAAATCACATGAATCGTTAA
1649496 ACGGACTTGTTAACAAATAAA
66 ACGGACTTGTTAACAAATAAA
1649517 A
1 A
1649518 TTGTTGGTAA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (86 bp):
AATGGAGTTGCCCTTGCCAACGACACATCCCACCTCAAGAGTGAACAAATCACATGAATCGTTAA
ACGGACTTGTTAACAAATAAA
Found at i:1653178 original size:243 final size:246
Alignment explanation
Indices: 1652742--1653241 Score: 970
Period size: 243 Copynumber: 2.0 Consensus size: 246
1652732 ACTCACCCAT
*
1652742 ATTTTTATTTTTAGGTTCATAATTGTTATTAGTGTCTTATGTGATCATAAAGGGTCAAAAATAAG
1 ATTTATATTTTTAGGTTCATAATTGTTATTAGTGTCTTATGTGATCATAAAGGGTCAAAAATAAG
1652807 GCTTTAAAACATGTTAAAAGCCTAAACCATGAAATCTATAATGAAAATGCTCAACATGCTTTAAA
66 GCTTTAAAACATGTTAAAAGCCTAAACCATGAAATCTATAATGAAAATGCTCAACATGCTTTAAA
1652872 CTCAGCTAATATGCTATCTTGCATTTCTAATGACCCACTAAAGGTATGAATGAGTTGTGAATGTG
131 CTCAGCTAATATGCTATCTTGCATTTCTAATGACCCACTAAAGGTATGAATGAGTTGTGAATGTG
1652937 TTACCCTGAATTCTTGGCTGCTAACGAAGCCCTCAAATCACTTAAGAGGCA
196 TTACCCTGAATTCTTGGCTGCTAACGAAGCCCTCAAATCACTTAAGAGGCA
1652988 ATTTATATTTTTAGGTTCATAATTGTTATTAGTGTCTTATGTGATCATAAAGGGTCAAAAATAAG
1 ATTTATATTTTTAGGTTCATAATTGTTATTAGTGTCTTATGTGATCATAAAGGGTCAAAAATAAG
1653053 GCTTT-AAACATGTTAAAAGCCTAAACCATGAAATCTATAATG-AAATGCTCAACATGC-TTAAA
66 GCTTTAAAACATGTTAAAAGCCTAAACCATGAAATCTATAATGAAAATGCTCAACATGCTTTAAA
1653115 CTCAGCTAATATGCTATCTTGCATTTCTAATGACCCACTAAAGGTATGAATGAGTTGTGAATGTG
131 CTCAGCTAATATGCTATCTTGCATTTCTAATGACCCACTAAAGGTATGAATGAGTTGTGAATGTG
1653180 TTACCCTGAATTCTTGGCTGCTAACGAAGCCCTCAAATCACTTAAGAGGCA
196 TTACCCTGAATTCTTGGCTGCTAACGAAGCCCTCAAATCACTTAAGAGGCA
1653231 ATTTATATTTT
1 ATTTATATTTT
1653242 CCCTTTGTTC
Statistics
Matches: 253, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
243 132 0.52
244 15 0.06
245 37 0.15
246 69 0.27
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (246 bp):
ATTTATATTTTTAGGTTCATAATTGTTATTAGTGTCTTATGTGATCATAAAGGGTCAAAAATAAG
GCTTTAAAACATGTTAAAAGCCTAAACCATGAAATCTATAATGAAAATGCTCAACATGCTTTAAA
CTCAGCTAATATGCTATCTTGCATTTCTAATGACCCACTAAAGGTATGAATGAGTTGTGAATGTG
TTACCCTGAATTCTTGGCTGCTAACGAAGCCCTCAAATCACTTAAGAGGCA
Found at i:1658129 original size:23 final size:23
Alignment explanation
Indices: 1658099--1658181 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
1658089 GTCGAGGGTT
*
1658099 CTATGTGGTCATTCGGGATAAAA
1 CTATGTGGTCCTTCGGGATAAAA
* *
1658122 CTATGTGGTCCTTTGGAATAAAA
1 CTATGTGGTCCTTCGGGATAAAA
*
1658145 CTATGTGGTCCTTCAGGAT-AAA
1 CTATGTGGTCCTTCGGGATAAAA
*
1658167 -TATGTGGTACTTCGG
1 CTATGTGGTCCTTCGG
1658182 TGTAAATTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 13 0.25
22 3 0.06
23 36 0.69
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGATAAAA
Found at i:1658747 original size:16 final size:16
Alignment explanation
Indices: 1658728--1658758 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1658718 TTCTCAAACT
*
1658728 TTTTAATAGTCAATGA
1 TTTTAAAAGTCAATGA
1658744 TTTTAAAAGTCAATG
1 TTTTAAAAGTCAATG
1658759 TGACACATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (16 bp):
TTTTAAAAGTCAATGA
Found at i:1659087 original size:13 final size:13
Alignment explanation
Indices: 1659069--1659107 Score: 62
Period size: 12 Copynumber: 3.1 Consensus size: 13
1659059 CATGCATATC
1659069 AGGGAGTGCCTGT
1 AGGGAGTGCCTGT
1659082 AGGGAGTG-CTGT
1 AGGGAGTGCCTGT
*
1659094 AGGGAGTGCTTGT
1 AGGGAGTGCCTGT
1659107 A
1 A
1659108 CAAGATAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.18, C:0.10, G:0.46, T:0.26
Consensus pattern (13 bp):
AGGGAGTGCCTGT
Found at i:1661336 original size:13 final size:13
Alignment explanation
Indices: 1661318--1661359 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1661308 TAGCATATTA
1661318 AAAATAAAACTTG
1 AAAATAAAACTTG
*
1661331 AAAATAAAA--GG
1 AAAATAAAACTTG
1661342 AAAATGAAAACTTG
1 AAAAT-AAAACTTG
1661356 AAAA
1 AAAA
1661360 AGTAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 6 0.25
12 4 0.17
13 9 0.38
14 5 0.21
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.17
Consensus pattern (13 bp):
AAAATAAAACTTG
Found at i:1664364 original size:24 final size:23
Alignment explanation
Indices: 1664337--1664389 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1664327 CCACTATGGG
*
1664337 CACATAGAATTTGTCCCGAAGGAC
1 CACATAGAA-TTCTCCCGAAGGAC
* **
1664361 CACATATAATTCTCCTTAAGGAC
1 CACATAGAATTCTCCCGAAGGAC
1664384 CACATA
1 CACATA
1664390 TATATTCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (23 bp):
CACATAGAATTCTCCCGAAGGAC
Found at i:1664404 original size:21 final size:21
Alignment explanation
Indices: 1664355--1664473 Score: 87
Period size: 21 Copynumber: 5.6 Consensus size: 21
1664345 ATTTGTCCCG
*
1664355 AAGGACCACATATAAT-TCTCCTT
1 AAGGACCACATAT-ATGT-TCC-A
*
1664378 AAGGACCACATATATATTCCA
1 AAGGACCACATATATGTTCCA
* *
1664399 AAGGACCAAATATGTGTTCCA
1 AAGGACCACATATATGTTCCA
* * **
1664420 ATGAACCGTATATATGTTCCA
1 AAGGACCACATATATGTTCCA
** * *
1664441 AAGGATTACATATATGTCCCG
1 AAGGACCACATATATGTTCCA
*
1664462 AATGACCACATA
1 AAGGACCACATA
1664474 GAACCCTCGA
Statistics
Matches: 75, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
21 56 0.75
22 5 0.07
23 14 0.19
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (21 bp):
AAGGACCACATATATGTTCCA
Found at i:1667442 original size:42 final size:42
Alignment explanation
Indices: 1667383--1667468 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
1667373 TTCATCTTTG
1667383 TTTTGCAATTCCTTAATTCGATCCAACCATGTTGACTTAAAC
1 TTTTGCAATTCCTTAATTCGATCCAACCATGTTGACTTAAAC
1667425 TTTTGCAATTCCTTAATTCGATCCAACCATGTTGACTTAAAC
1 TTTTGCAATTCCTTAATTCGATCCAACCATGTTGACTTAAAC
1667467 TT
1 TT
1667469 CAATTCTGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (42 bp):
TTTTGCAATTCCTTAATTCGATCCAACCATGTTGACTTAAAC
Found at i:1677659 original size:59 final size:60
Alignment explanation
Indices: 1677545--1677707 Score: 165
Period size: 60 Copynumber: 2.8 Consensus size: 60
1677535 TTTGGGGATG
* ** * * * *
1677545 AAATTAGAGTATTTAAAAGTTTAGGGATCAACTTAGAAA-GTG-GTCATAGTTTAGAGATA
1 AAATTAGAATATTCCAAAGTTTAAGGATCAATTTA-AAATGAGAGTAATAGTTTAGAGATA
* *
1677604 AAA-TAGAATGTT-CAAACGTTTAAGGA-CTAATTTAGAATGAGAGTAATAGTTTAGAGATA
1 AAATTAGAATATTCCAAA-GTTTAAGGATC-AATTTAAAATGAGAGTAATAGTTTAGAGATA
* *
1677663 AAATTGGAATATTCCAAAGTTTAATGATCAATTTAAAATGAGAGT
1 AAATTAGAATATTCCAAAGTTTAAGGATCAATTTAAAATGAGAGT
1677708 TATAATTTGG
Statistics
Matches: 85, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
57 6 0.07
58 22 0.26
59 22 0.26
60 30 0.35
61 5 0.06
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.32
Consensus pattern (60 bp):
AAATTAGAATATTCCAAAGTTTAAGGATCAATTTAAAATGAGAGTAATAGTTTAGAGATA
Found at i:1679270 original size:20 final size:20
Alignment explanation
Indices: 1679247--1679284 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1679237 CTCTGATAAG
*
1679247 GGTATCGCTACTCCTGAGCT
1 GGTATCGATACTCCTGAGCT
*
1679267 GGTATCGATACTGCTGAG
1 GGTATCGATACTCCTGAG
1679285 TCAGCATCGA
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:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (20 bp):
GGTATCGATACTCCTGAGCT
Found at i:1681601 original size:23 final size:23
Alignment explanation
Indices: 1681561--1681619 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
1681551 TAAGAATAAT
* *
1681561 TCTACTTTTATGAAACATTCATC
1 TCTACTTTTGTGGAACATTCATC
* *
1681584 TCTACTTTTGTGGCACATTTATC
1 TCTACTTTTGTGGAACATTCATC
* *
1681607 GCTACCTTTGTGG
1 TCTACTTTTGTGG
1681620 TACTGTAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (23 bp):
TCTACTTTTGTGGAACATTCATC
Found at i:1690593 original size:4 final size:4
Alignment explanation
Indices: 1690580--1690609 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1690570 ATTGGTTATC
1690580 TTAA -TAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
1690610 TCACGTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:1692191 original size:21 final size:21
Alignment explanation
Indices: 1692157--1692221 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
1692147 TTACTATAAG
*
1692157 ATTTA-AAATAAAATTTTAAT
1 ATTTATAAATTAAATTTTAAT
*
1692177 ATTTATAAATTAAATTTTGAT
1 ATTTATAAATTAAATTTTAAT
* *
1692198 ATGTATAAAATAAA-TTTAAT
1 ATTTATAAATTAAATTTTAAT
1692218 ATTT
1 ATTT
1692222 TTTAAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (21 bp):
ATTTATAAATTAAATTTTAAT
Found at i:1692227 original size:21 final size:21
Alignment explanation
Indices: 1692158--1692235 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
1692148 TACTATAAGA
1692158 TTTAAAATAAAATTTTAATATT
1 TTTAAAAT-AAATTTTAATATT
* * * *
1692180 TATAAATTAAATTTTGATATG
1 TTTAAAATAAATTTTAATATT
*
1692201 TATAAAATAAA-TTTAATATTT
1 TTTAAAATAAATTTTAATA-TT
1692222 TTTAAAAT-AATTTT
1 TTTAAAATAAATTTT
1692236 GAAAATTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 8 0.17
21 32 0.70
22 6 0.13
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTAAAATAAATTTTAATATT
Found at i:1703358 original size:21 final size:21
Alignment explanation
Indices: 1703334--1703393 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
1703324 GGATTGTGAG
1703334 GATGAGGTGTGTCCAGTGATT
1 GATGAGGTGTGTCCAGTGATT
*
1703355 GATGAGGTGTGTCCAGTGCTT
1 GATGAGGTGTGTCCAGTGATT
1703376 GATGAGGTGTGTCCAGTG
1 GATGAGGTGTGTCCAGTG
1703394 TTTATTCCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.17, C:0.12, G:0.40, T:0.32
Consensus pattern (21 bp):
GATGAGGTGTGTCCAGTGATT
Found at i:1706790 original size:17 final size:16
Alignment explanation
Indices: 1706756--1706793 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
1706746 GTTTAAAAAA
1706756 TAAAAAATAAAAATAT
1 TAAAAAATAAAAATAT
1706772 TAAATAAATAAAAGA-AT
1 TAAA-AAATAAAA-ATAT
1706789 TAAAA
1 TAAAA
1706794 GACAATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 14 0.70
18 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAAATAAAAATAT
Found at i:1707563 original size:2 final size:2
Alignment explanation
Indices: 1707558--1707826 Score: 83
Period size: 2 Copynumber: 141.5 Consensus size: 2
1707548 AAAATAAATA
*
1707558 AT AT AT A- AT AT AT GAT AT A- AT ACT AT -T AT A- AT AT GT AT AT
1 AT AT AT AT AT AT AT -AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
*
1707598 AT AG A- AT AT AT AT AT AT AT ACT AT AT A- AT AT A- AT ACT AT ACT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT A-T
*
1707640 AT AT A- AA AT A- AT AT AT A- AT AT A- AT ACT AT ACT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT
* *
1707679 AT AT A- AC AC A- AT ACT AT A- AT AT A- AT ACT AT A- AT AT AT A-
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
1707717 AT ACC AT A- AT AT AT A- AT ACC AT AT A- AC AT AT AT -T AT AT ACT
1 AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T
* * * *
1707758 AT AT AA AT ACT AT A- AT AT AT GT -T AT AC A- AT AT ACC AT ACT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T
*
1707798 AT A- AT AT AT AT -T AT AT A- AA AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1707827 ACATATAATA
Statistics
Matches: 207, Mismatches: 16, Indels: 88
0.67 0.05 0.28
Matches are distributed among these distances:
1 29 0.14
2 151 0.73
3 27 0.13
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:1707565 original size:7 final size:7
Alignment explanation
Indices: 1707550--1707836 Score: 167
Period size: 7 Copynumber: 39.6 Consensus size: 7
1707540 TTAATAAAAA
*
1707550 AATAAAT
1 AATATAT
1707557 AATATAT
1 AATATAT
1707564 AATATAT
1 AATATAT
*
1707571 GATATAAT
1 AATAT-AT
*
1707579 ACTATTAT
1 AATA-TAT
*
1707587 AATATGT
1 AATATAT
*
1707594 ATATATAG
1 A-ATATAT
1707602 AATATAT
1 AATATAT
1707609 ATATATAT
1 A-ATATAT
*
1707617 ACTATAT
1 AATATAT
1707624 -A-ATAT
1 AATATAT
1707629 AATACTAT
1 AATA-TAT
*
1707637 ACTATAT
1 AATATAT
1707644 AA-A-AT
1 AATATAT
1707649 AATATAT
1 AATATAT
1707656 -A-ATAT
1 AATATAT
1707661 AATACTAT
1 AATA-TAT
*
1707669 ACTATAT
1 AATATAT
1707676 AATATAT
1 AATATAT
* *
1707683 AACACAAT
1 AATA-TAT
1707691 ACTATAATAT
1 A--AT-ATAT
1707701 AATACTAT
1 AATA-TAT
1707709 AATATAT
1 AATATAT
*
1707716 AATACCAT
1 AATA-TAT
1707724 AATATAT
1 AATATAT
1707731 AATACCATAT
1 AAT---ATAT
*
1707741 AACATAT
1 AATATAT
*
1707748 ATTATAT
1 AATATAT
*
1707755 ACTATAT
1 AATATAT
1707762 AAATACTAT
1 -AATA-TAT
1707771 AATATAT
1 AATATAT
** *
1707778 GTTATAC
1 AATATAT
*
1707785 AATATAC
1 AATATAT
*
1707792 CATACTAT
1 AATA-TAT
1707800 AATATAT
1 AATATAT
*
1707807 ATTATAT
1 AATATAT
1707814 AA-A-AT
1 AATATAT
1707819 AATATAT
1 AATATAT
*
1707826 AACATAT
1 AATATAT
1707833 AATA
1 AATA
1707837 GTGTATATTA
Statistics
Matches: 216, Mismatches: 38, Indels: 52
0.71 0.12 0.17
Matches are distributed among these distances:
5 16 0.07
6 7 0.03
7 115 0.53
8 63 0.29
9 4 0.02
10 10 0.05
11 1 0.00
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (7 bp):
AATATAT
Found at i:1707607 original size:20 final size:19
Alignment explanation
Indices: 1707555--1707836 Score: 114
Period size: 20 Copynumber: 13.6 Consensus size: 19
1707545 AAAAAAATAA
1707555 ATAATATATAATATATGATAT
1 ATAA-ATATAATATAT-ATAT
* *
1707576 AATACTATTATAATATGTATAT
1 -ATA--AATATAATATATATAT
1707598 ATAGAATATATATATATATACT
1 ATA-AATATA-ATATATATA-T
1707620 ATATAATATAATACTATACTAT
1 ATA-AATATAATA-TATA-TAT
1707642 ATAAA-ATAATATATA-AT
1 ATAAATATAATATATATAT
*
1707659 ATAATACTATACTATATA-AT
1 ATAA-A-TATAATATATATAT
* *
1707679 ATATAACACAATACTATA-AT
1 ATA-AATATAATA-TATATAT
1707699 ATAATACTATAATATATA-AT
1 ATAA-A-TATAATATATATAT
* *
1707719 ACCATAATAT-ATA-ATACCAT
1 A-TA-AATATAATATATA-TAT
*
1707739 ATAACATATATTATATACTAT
1 ATAA-ATATAATATATA-TAT
*
1707760 ATAAATACT-ATAATATATGTT
1 ATAAATA-TAAT-ATATAT-AT
1707781 ATACAATATACCATACTATAATAT
1 ATA-AATATA--ATA-TAT-ATAT
* *
1707805 ATATTATATAAAATA-ATAT
1 ATA-AATATAATATATATAT
1707824 ATAACATATAATA
1 ATAA-ATATAATA
1707837 GTGTATATTA
Statistics
Matches: 206, Mismatches: 24, Indels: 63
0.70 0.08 0.22
Matches are distributed among these distances:
17 6 0.03
18 5 0.02
19 31 0.15
20 56 0.27
21 47 0.23
22 32 0.16
23 12 0.06
24 15 0.07
25 2 0.01
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (19 bp):
ATAAATATAATATATATAT
Found at i:1707611 original size:15 final size:15
Alignment explanation
Indices: 1707555--1707851 Score: 141
Period size: 15 Copynumber: 19.3 Consensus size: 15
1707545 AAAAAAATAA
1707555 ATAATATATA-ATAT
1 ATAATATATATATAT
*
1707569 ATGATATA-ATACTATT
1 ATAATATATATA-TA-T
*
1707585 ATAATATGTATATAT
1 ATAATATATATATAT
*
1707600 AGAATATATATATAT
1 ATAATATATATATAT
*
1707615 AT-A-CTATATA-AT
1 ATAATATATATATAT
1707627 ATAATACTATACTATAT
1 ATAATA-TATA-TATAT
*
1707644 AAAATA-ATATATAAT
1 ATAATATATATAT-AT
*
1707659 ATAATACTATA-CTAT
1 ATAATA-TATATATAT
* *
1707674 ATAATATATA-ACACA
1 ATAATATATATATA-T
*
1707689 ATACTATAATATAATACT
1 ATAATAT-ATAT-ATA-T
*
1707707 ATAATATATA-ATACC
1 ATAATATATATATA-T
*
1707722 ATAATATATAATACCAT
1 ATAATATAT-ATA-TAT
*
1707739 ATAACATATAT-TAT
1 ATAATATATATATAT
* *
1707753 ATACTATATAAATACT
1 ATAATATATATATA-T
*
1707769 ATAATATATGT-TAT
1 ATAATATATATATAT
* * *
1707783 ACAATATACCATA-CT
1 ATAATATA-TATATAT
1707798 ATAATATATATTATAT
1 ATAATATATA-TATAT
* *
1707814 AAAATAATATATAACAT
1 ATAAT-ATATAT-ATAT
*
1707831 ATAATAGTGTATATTAT
1 ATAATA-TATATA-TAT
1707848 ATAA
1 ATAA
1707852 AAAAATCCGG
Statistics
Matches: 213, Mismatches: 41, Indels: 55
0.69 0.13 0.18
Matches are distributed among these distances:
12 4 0.02
13 8 0.04
14 36 0.17
15 73 0.34
16 35 0.16
17 47 0.22
18 10 0.05
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (15 bp):
ATAATATATATATAT
Found at i:1707628 original size:5 final size:5
Alignment explanation
Indices: 1707560--1707836 Score: 57
Period size: 5 Copynumber: 54.6 Consensus size: 5
1707550 AATAAATAAT
* * *
1707560 ATATA ATATA TGATATA ATACTA TTATA ATAT- GTATA TATAGA ATAT-
1 ATATA ATATA --ATATA ATA-TA ATATA ATATA ATATA -ATATA ATATA
*
1707607 ATATA TATATA CTATATA ATATA ATACT- ATACT- ATATA AAATAA TATATA
1 ATATA -ATATA --ATATA ATATA ATA-TA ATA-TA ATATA ATAT-A -ATATA
* *
1707657 ATATA ATACT- ATACT- ATATA ATAT- ATA-A CACAATA CTATA ATATA
1 ATATA ATA-TA ATA-TA ATATA ATATA ATATA -A-TATA ATATA ATATA
** ** *
1707702 ATACT- ATA-A TATATA ATACC ATA-A TATATA ATACC ATATA ACAT-
1 ATA-TA ATATA -ATATA ATATA ATATA -ATATA ATATA ATATA ATATA
* * * * * **
1707746 ATATT ATATA CTATATA A-ATA CTATA ATAT- ATGTT ATACA ATATA CCATA
1 ATATA ATATA --ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * *
1707796 CTATA ATAT- ATATT ATATA AAATA ATAT- ATA-A CATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA -ATATA ATA
1707837 GTGTATATTA
Statistics
Matches: 203, Mismatches: 36, Indels: 66
0.67 0.12 0.22
Matches are distributed among these distances:
4 28 0.14
5 134 0.66
6 21 0.10
7 20 0.10
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:1707702 original size:72 final size:74
Alignment explanation
Indices: 1707621--1707776 Score: 196
Period size: 75 Copynumber: 2.1 Consensus size: 74
1707611 ATATATACTA
* *
1707621 TATAATATAATACTATACTATATAA-A-ATAATATATAATATAATACTATAC-TATATAATATA-
1 TATAATATAATACTATAATATATAATACATAATATATAATACAATA-TA-ACATATATAATATAC
1707682 TA-ACACAATAC
64 TATACA-AATAC
* *
1707693 TATAATATAATACTATAATATATAATACCATAATATATAATACCATATAACATATATTATATACT
1 TATAATATAATACTATAATATATAATA-CATAATATATAATACAATATAACATATATAATATACT
*
1707758 ATATAAATAC
65 ATACAAATAC
1707768 TATAATATA
1 TATAATATA
1707777 TGTTATACAA
Statistics
Matches: 73, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
72 24 0.33
73 3 0.04
74 12 0.16
75 32 0.44
76 2 0.03
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (74 bp):
TATAATATAATACTATAATATATAATACATAATATATAATACAATATAACATATATAATATACTA
TACAAATAC
Found at i:1707820 original size:19 final size:19
Alignment explanation
Indices: 1707798--1707853 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
1707788 ATACCATACT
1707798 ATAATATATATTATATAAA
1 ATAATATATATTATATAAA
* *
1707817 ATAATATATA--ACATATA
1 ATAATATATATTATATAAA
* *
1707834 ATAGTGTATATTATATAAA
1 ATAATATATATTATATAAA
1707853 A
1 A
1707854 AAATCCGGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 13 0.45
19 16 0.55
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (19 bp):
ATAATATATATTATATAAA
Found at i:1707823 original size:17 final size:18
Alignment explanation
Indices: 1707803--1707853 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
1707793 ATACTATAAT
1707803 ATATATTATATAAAATA-
1 ATATATTATATAAAATAG
* * *
1707820 ATATATAACATATAATAG
1 ATATATTATATAAAATAG
*
1707838 TGTATATTATATAAAA
1 -ATATATTATATAAAA
1707854 AAATCCGGAA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
17 14 0.56
19 11 0.44
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (18 bp):
ATATATTATATAAAATAG
Found at i:1709541 original size:25 final size:25
Alignment explanation
Indices: 1709490--1709566 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 25
1709480 ATTTTAGACA
**
1709490 TATTAACTTAAAAAATAT-TTTTA-
1 TATTAACTTATTAAATATATTTTAT
1709513 TATTAACTTATTAAATATATTTTAT
1 TATTAACTTATTAAATATATTTTAT
*
1709538 TATTAACTTAATTTTAAAAATATTTTAT
1 TATTAACTT-A--TTAAATATATTTTAT
1709566 T
1 T
1709567 TTATTTTCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
23 16 0.35
24 5 0.11
25 9 0.20
26 1 0.02
28 15 0.33
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTAACTTATTAAATATATTTTAT
Found at i:1709587 original size:27 final size:29
Alignment explanation
Indices: 1709501--1709594 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 29
1709491 ATTAACTTAA
1709501 AAAATAT-TTTTA-TATTAACTT-A--TT
1 AAAATATATTTTATTATTAACTTAATTTT
1709525 -AAATATATTTTATTATTAACTTAATTTT
1 AAAATATATTTTATTATTAACTTAATTTT
** * *
1709553 AAAA-ATATTTTATT-TTATTTTCATTTA
1 AAAATATATTTTATTATTAACTTAATTTT
1709580 AAATATATATTTTAT
1 AAA-ATATATTTTAT
1709595 GTTAAAATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
23 6 0.10
24 5 0.09
25 9 0.16
26 1 0.02
27 12 0.21
28 13 0.22
29 12 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
AAAATATATTTTATTATTAACTTAATTTT
Found at i:1709706 original size:116 final size:115
Alignment explanation
Indices: 1709571--1709803 Score: 412
Period size: 116 Copynumber: 2.0 Consensus size: 115
1709561 TTTATTTTAT
* * *
1709571 TTTCATTTAAAATATATATTTTATGTTAAAATTTATTTAAAAGTATGACTAAATTGAGATAATAT
1 TTTCATTTAAAATATATATTTTATGTTAAAATTTATTTAAAAGTATAACTAAATTAAGAGAATAT
* *
1709636 GTAAATAACAGAGACCAAATGTGTGATTATACAAACTATCATGTCACATA
66 GTAAATAACAAAGACCAAATGTGTGATTATACAAACTATCACGTCACATA
1709686 TTTCATTTAAAAATATATATTTTATGTTAAAATTTATTTAAAAGTATAACTAAATTAAGAGAATA
1 TTTCATTT-AAAATATATATTTTATGTTAAAATTTATTTAAAAGTATAACTAAATTAAGAGAATA
1709751 TGTAAATAACAAAGACCAAATGTGTGATTATACAAACTATCACGTCACATA
65 TGTAAATAACAAAGACCAAATGTGTGATTATACAAACTATCACGTCACATA
1709802 TT
1 TT
1709804 CTGTTAATTG
Statistics
Matches: 112, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
115 8 0.07
116 104 0.93
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (115 bp):
TTTCATTTAAAATATATATTTTATGTTAAAATTTATTTAAAAGTATAACTAAATTAAGAGAATAT
GTAAATAACAAAGACCAAATGTGTGATTATACAAACTATCACGTCACATA
Found at i:1710458 original size:60 final size:61
Alignment explanation
Indices: 1710347--1710464 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 61
1710337 TCCTTAAATT
* * *
1710347 TAATTTAATTTTATCCCCAAATTATGGCTCTCATTTTAAATGAATCTTTAAA-CTTTTGAA
1 TAATTTAATTTTATCCCCAAATTATGGCTCTCATTCTAAATGAAGCCTTAAACCTTTTGAA
* *
1710407 TAATTTAATTTTATCCCCAAATTATGGCTCTCATTCTAAATTAGGCCTTAAACCTTTT
1 TAATTTAATTTTATCCCCAAATTATGGCTCTCATTCTAAATGAAGCCTTAAACCTTTT
1710465 AAAATTCCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
60 47 0.90
61 5 0.10
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (61 bp):
TAATTTAATTTTATCCCCAAATTATGGCTCTCATTCTAAATGAAGCCTTAAACCTTTTGAA
Found at i:1713887 original size:11 final size:11
Alignment explanation
Indices: 1713871--1713902 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1713861 ATTATCAATA
1713871 AAAAAATATAT
1 AAAAAATATAT
1713882 AAAAAATATAT
1 AAAAAATATAT
*
1713893 AAAATATATA
1 AAAAAATATA
1713903 ATAATTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAAAATATAT
Found at i:1713892 original size:13 final size:12
Alignment explanation
Indices: 1713868--1713896 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1713858 CATATTATCA
1713868 ATAAAAAAATAT
1 ATAAAAAAATAT
1713880 AT-AAAAAATAT
1 ATAAAAAAATAT
1713891 ATAAAA
1 ATAAAA
1713897 TATATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAAAAATAT
Found at i:1743395 original size:14 final size:14
Alignment explanation
Indices: 1743376--1743421 Score: 92
Period size: 14 Copynumber: 3.3 Consensus size: 14
1743366 CGTTCGTGAA
1743376 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1743390 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1743404 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1743418 CGTT
1 CGTT
1743422 TATGTTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.07, C:0.15, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1743438 original size:24 final size:24
Alignment explanation
Indices: 1743391--1743441 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1743381 GGTTATGTTC
* *
1743391 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
* *
1743415 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
1743439 GTT
1 GTT
1743442 TAACCCAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCAGTTAT
Found at i:1744473 original size:10 final size:10
Alignment explanation
Indices: 1744458--1744532 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1744448 GGGTCTCCAA
1744458 CGTTTATGTT
1 CGTTTATGTT
1744468 CGTTTATGTT
1 CGTTTATGTT
1744478 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
1744489 ATGTTCGTGTT
1 -CGTTTATGTT
1744500 CGTTTATGTT
1 CGTTTATGTT
1744510 CG----TGTT
1 CGTTTATGTT
1744516 CGTTTATGTT
1 CGTTTATGTT
1744526 CGTTTAT
1 CGTTTAT
1744533 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1744489 original size:16 final size:16
Alignment explanation
Indices: 1744464--1744528 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1744454 CCAACGTTTA
1744464 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1744480 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
1744496 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1744512 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1744528 T
1 T
1744529 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1744618 original size:16 final size:16
Alignment explanation
Indices: 1744597--1744629 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1744587 AAAAAAAAAT
1744597 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1744613 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1744629 T
1 T
1744630 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1745911 original size:26 final size:26
Alignment explanation
Indices: 1745882--1745931 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1745872 GAGAACCGGA
*
1745882 AACGAGCTTGTTCATGAACATAAATG
1 AACGAGCTTATTCATGAACATAAATG
*
1745908 AACGAGCTTATTCGTGAACATAAA
1 AACGAGCTTATTCATGAACATAAA
1745932 CGAAACGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (26 bp):
AACGAGCTTATTCATGAACATAAATG
Found at i:1748549 original size:63 final size:62
Alignment explanation
Indices: 1748470--1748595 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 62
1748460 CATTTTAAAT
* ** * *
1748470 TAGTTCTTAAACTTTTGAATGTTCTAATTCCATCCCTAAACTATGACTCTCGTTCTAGATTAC
1 TAGTCCTTAAACTTTTGAACATTCTAATTCCAT-CCTAAACTATGACTATCGTTCTAAATTAC
* * *
1748533 TAGTCCTTAAACTTTTGAACATTCTAATTTCATCCTAAACTATGATTATCTTTCTAAATTAC
1 TAGTCCTTAAACTTTTGAACATTCTAATTCCATCCTAAACTATGACTATCGTTCTAAATTAC
1748595 T
1 T
1748596 CCCCAAATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
62 26 0.47
63 29 0.53
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (62 bp):
TAGTCCTTAAACTTTTGAACATTCTAATTCCATCCTAAACTATGACTATCGTTCTAAATTAC
Found at i:1752644 original size:22 final size:21
Alignment explanation
Indices: 1752616--1752671 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 21
1752606 GTACCCTTAT
1752616 GGGGTATCGATACACATTCAAA
1 GGGGTATCGATACACATT-AAA
*
1752638 GGGGTATCGATACACGTTAAA
1 GGGGTATCGATACACATTAAA
*
1752659 GAGGTATCGATAC
1 GGGGTATCGATAC
1752672 CTAGTGCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (21 bp):
GGGGTATCGATACACATTAAA
Found at i:1752664 original size:21 final size:22
Alignment explanation
Indices: 1752618--1752671 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
1752608 ACCCTTATGG
*
1752618 GGTATCGATACACATTCAAAGG
1 GGTATCGATACACATTCAAAGA
*
1752640 GGTATCGATACACGTT-AAAGA
1 GGTATCGATACACATTCAAAGA
1752661 GGTATCGATAC
1 GGTATCGATAC
1752672 CTAGTGCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (22 bp):
GGTATCGATACACATTCAAAGA
Found at i:1758416 original size:20 final size:20
Alignment explanation
Indices: 1758391--1758444 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1758381 TAAATGACTA
*
1758391 GGGGTATTGGTACCTCTAAG
1 GGGGTATCGGTACCTCTAAG
1758411 GGGGTATCGGTACCTCTAAG
1 GGGGTATCGGTACCTCTAAG
1758431 GGGGTATCGGTACC
1 GGGGTATCGGTACC
1758445 CATAGGGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.19, C:0.19, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGTATCGGTACCTCTAAG
Found at i:1758999 original size:19 final size:19
Alignment explanation
Indices: 1758972--1759010 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1758962 TCTTAAACTT
*
1758972 TCTATTATTTTATAATAAA
1 TCTAATATTTTATAATAAA
*
1758991 TCTAATATTTTTTAATAAA
1 TCTAATATTTTATAATAAA
1759010 T
1 T
1759011 TATCAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:1759181 original size:16 final size:16
Alignment explanation
Indices: 1759160--1759190 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1759150 ATTCGAGTTT
*
1759160 CTTTTGGTTTGGGTTG
1 CTTTTGGTTCGGGTTG
1759176 CTTTTGGTTCGGGTT
1 CTTTTGGTTCGGGTT
1759191 AATTTTAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.10, G:0.35, T:0.55
Consensus pattern (16 bp):
CTTTTGGTTCGGGTTG
Found at i:1759583 original size:22 final size:21
Alignment explanation
Indices: 1759530--1759579 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
1759520 ACAATACTAT
**
1759530 ACAGTATGAACAGTATTATGA
1 ACAGTATGAACAGTACCATGA
*
1759551 ACAGTAGTGAACAGTACCGTGA
1 ACAGTA-TGAACAGTACCATGA
1759573 ACAGTAT
1 ACAGTAT
1759580 TGAATGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (21 bp):
ACAGTATGAACAGTACCATGA
Found at i:1761629 original size:21 final size:21
Alignment explanation
Indices: 1761591--1761632 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1761581 TTCCCATAAA
**
1761591 TCACTATTCATGCACGAAAAT
1 TCACTATTCAAACACGAAAAT
*
1761612 TCACTATTCAAACCCGAAAAT
1 TCACTATTCAAACACGAAAAT
1761633 CATCAACTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (21 bp):
TCACTATTCAAACACGAAAAT
Done.