Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 24
Found at i:2837481 original size:20 final size:21
Alignment explanation
Indices: 2837457--2837610 Score: 78
Period size: 20 Copynumber: 7.6 Consensus size: 21
2837447 AGTTTCCAAT
2837457 TTCGCAACGCGAATATGTAAA
1 TTCGCAACGCGAATATGTAAA
** * * **
2837478 -TCGCATTGCGATTTTCCAAA
1 TTCGCAACGCGAATATGTAAA
*
2837498 TTCGCAACGTGAA-A-GTCAAA
1 TTCGCAACGCGAATATGT-AAA
*
2837518 TTCGCAACGCGAATTTGTAAA
1 TTCGCAACGCGAATATGTAAA
* *
2837539 -TCACAACAC-AGA-A-GTCAAA
1 TTCGCAACGCGA-ATATGT-AAA
2837558 TTCGCAACGCG-ATA-GTCAAA
1 TTCGCAACGCGAATATGT-AAA
* *
2837578 TTCGCAACACG-ATAAT-CAAA
1 TTCGCAACGCGAAT-ATGTAAA
2837598 TTCGCAACGCGAA
1 TTCGCAACGCGAA
2837611 AGTCAAATGT
Statistics
Matches: 98, Mismatches: 23, Indels: 24
0.68 0.16 0.17
Matches are distributed among these distances:
18 2 0.02
19 5 0.05
20 76 0.78
21 13 0.13
22 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (21 bp):
TTCGCAACGCGAATATGTAAA
Found at i:2837616 original size:20 final size:20
Alignment explanation
Indices: 2837494--2837618 Score: 132
Period size: 20 Copynumber: 6.2 Consensus size: 20
2837484 TGCGATTTTC
*
2837494 CAAATTCGCAACGTGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
2837514 CAAATTCGCAACGCGAATTTGT
1 CAAATTCGCAACGCGAA--AGT
* *
2837536 -AAA-TCACAACAC-AGAAGT
1 CAAATTCGCAACGCGA-AAGT
*
2837554 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
2837574 CAAATTCGCAACACGATAA-T
1 CAAATTCGCAACGCGA-AAGT
2837594 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
2837614 CAAAT
1 CAAAT
2837619 GTTTTTACGC
Statistics
Matches: 86, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
18 2 0.02
19 6 0.07
20 71 0.83
21 5 0.06
22 2 0.02
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:2839963 original size:63 final size:62
Alignment explanation
Indices: 2839866--2839985 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 62
2839856 AGGTCGGTAC
* *
2839866 TTTACGTGAAGATAATGGTGCATGGAGTGATGAGGT-TCGATCTTTACGTGGTGAGGTGGATTT
1 TTTACGCGAAGATAATGGTGCAT-GAGTGATGAGGTATCGA-CTTTACGTGATGAGGTGGATTT
* * *
2839929 TTTACGCGATGATAATGGTGCACT-ATGTGGTGAGGTATCTACTTTACGTGATGAGGT
1 TTTACGCGAAGATAATGGTGCA-TGA-GTGATGAGGTATCGACTTTACGTGATGAGGT
2839986 TGCCGCTCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
62 1 0.02
63 44 0.90
64 4 0.08
ACGTcount: A:0.23, C:0.10, G:0.33, T:0.35
Consensus pattern (62 bp):
TTTACGCGAAGATAATGGTGCATGAGTGATGAGGTATCGACTTTACGTGATGAGGTGGATTT
Found at i:2840321 original size:42 final size:42
Alignment explanation
Indices: 2840273--2840372 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
2840263 CGATGCACCT
* *
2840273 GTCATCATTCAAGAGGCTC-CTCCTATCGTTCAAGAGGCCCCTC
1 GTCATCATTCAAGAGGC-CACTCCCACCGTTCAAGAGGCCCC-C
*
2840316 -TCATCA-TCGAAGAAGCCACTCCCACCGTTCAAGAGGCCCCC
1 GTCATCATTC-AAGAGGCCACTCCCACCGTTCAAGAGGCCCCC
*
2840357 GTCATCGTTCAAGAGG
1 GTCATCATTCAAGAGG
2840373 TCCCGTCCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
41 4 0.08
42 42 0.88
43 2 0.04
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (42 bp):
GTCATCATTCAAGAGGCCACTCCCACCGTTCAAGAGGCCCCC
Found at i:2840365 original size:21 final size:21
Alignment explanation
Indices: 2840274--2840372 Score: 82
Period size: 21 Copynumber: 4.7 Consensus size: 21
2840264 GATGCACCTG
*
2840274 TCATCATTCAAGAGGCTCCTCC
1 TCATCGTTCAAGAGGC-CCTCC
2840296 T-ATCGTTCAAGAGGCCC-CTC
1 TCATCGTTCAAGAGGCCCTC-C
* *
2840316 TCATC-ATCGAAGAAGCCACTCC
1 TCATCGTTC-AAGAGGCC-CTCC
*
2840338 -CACCGTTCAAGAGGCCC-CC
1 TCATCGTTCAAGAGGCCCTCC
2840357 GTCATCGTTCAAGAGG
1 -TCATCGTTCAAGAGG
2840373 TCCCGTCCGC
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
19 3 0.05
20 7 0.11
21 46 0.74
22 5 0.08
23 1 0.02
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.21
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCTCC
Found at i:2840386 original size:21 final size:21
Alignment explanation
Indices: 2840338--2840392 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2840328 AAGCCACTCC
2840338 CACCGTTCAAGAGGCCCCCGT
1 CACCGTTCAAGAGGCCCCCGT
* *
2840359 CATCGTTCAAGAGG-TCCCGT
1 CACCGTTCAAGAGGCCCCCGT
*
2840379 CCGCCGTTCAAGAG
1 -CACCGTTCAAGAG
2840393 CCCGATGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 5 0.17
21 24 0.83
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.18
Consensus pattern (21 bp):
CACCGTTCAAGAGGCCCCCGT
Found at i:2841982 original size:20 final size:20
Alignment explanation
Indices: 2841954--2841996 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2841944 AATTTTTGGT
2841954 TTGCAAATTTGACTTTCACG
1 TTGCAAATTTGACTTTCACG
*
2841974 TTGCGAATTTGACTTTCACG
1 TTGCAAATTTGACTTTCACG
2841994 TTG
1 TTG
2841997 ATCGCAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (20 bp):
TTGCAAATTTGACTTTCACG
Found at i:2842227 original size:39 final size:39
Alignment explanation
Indices: 2842172--2842297 Score: 225
Period size: 39 Copynumber: 3.2 Consensus size: 39
2842162 TCAAGTTGTA
*
2842172 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
* *
2842211 AATTTTGATTTTCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
2842250 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
2842289 GATTTTGAT
1 GATTTTGAT
2842298 GAGCATCGGA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
Found at i:2842626 original size:24 final size:25
Alignment explanation
Indices: 2842599--2842651 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
2842589 AGTGGAGCCG
*
2842599 AAATTTG-TATTGAAATTCAAACTC
1 AAATTTGAAATTGAAATTCAAACTC
*
2842623 AAA-TTGAAATTTAAATTCAAACTC
1 AAATTTGAAATTGAAATTCAAACTC
*
2842647 CAATT
1 AAATT
2842652 ACATATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 3 0.12
24 20 0.83
25 1 0.04
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (25 bp):
AAATTTGAAATTGAAATTCAAACTC
Found at i:2842630 original size:18 final size:18
Alignment explanation
Indices: 2842607--2842643 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2842597 CGAAATTTGT
2842607 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2842625 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2842643 A
1 A
2842644 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2843064 original size:25 final size:25
Alignment explanation
Indices: 2843030--2843079 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2843020 ATTATTTTTC
*
2843030 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2843055 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2843080 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:2843201 original size:20 final size:20
Alignment explanation
Indices: 2843146--2843192 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2843136 TGTTGAAGGT
* * *
2843146 AAATTCGCAACGTGAAAGTC
1 AAATTCGCTACGCGATAGTC
2843166 AAATTCGCTACGCGATAGTC
1 AAATTCGCTACGCGATAGTC
2843186 AAATTCG
1 AAATTCG
2843193 GTTTGCGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
AAATTCGCTACGCGATAGTC
Found at i:2843235 original size:20 final size:20
Alignment explanation
Indices: 2843212--2843267 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2843202 TTCGCGTTTT
2843212 GAATTTGACTATCGCATTGC
1 GAATTTGACTATCGCATTGC
* * * *
2843232 GAATTTGTCTTTTGCGTTGC
1 GAATTTGACTATCGCATTGC
2843252 GAATTTGACTATCGCA
1 GAATTTGACTATCGCA
2843268 ATGCTTATTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
GAATTTGACTATCGCATTGC
Found at i:2845911 original size:24 final size:24
Alignment explanation
Indices: 2845877--2845930 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2845867 CCATCACATC
2845877 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2845901 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2845925 ATCAAA
1 ATCAAA
2845931 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2846947 original size:20 final size:19
Alignment explanation
Indices: 2846924--2846972 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
2846914 TGGAAACTGG
2846924 GTTGCGCAATTAGA-ATTCGC
1 GTTGCG-AATTAGAGA-TCGC
*
2846944 GTTGCGAATTTGAGATCGC
1 GTTGCGAATTAGAGATCGC
2846963 GTTGCGAATT
1 GTTGCGAATT
2846973 TGTTGGTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (19 bp):
GTTGCGAATTAGAGATCGC
Found at i:2848693 original size:31 final size:31
Alignment explanation
Indices: 2848644--2848741 Score: 133
Period size: 31 Copynumber: 3.2 Consensus size: 31
2848634 AGCAAATTAG
* *
2848644 TCACTAACATTATCGATTTGTAACAAACTAA
1 TCACTAACGTTATCGATTTGTAACAAAATAA
* * *
2848675 TCACTAATGTTATTGATTTGTAACAAAATGA
1 TCACTAACGTTATCGATTTGTAACAAAATAA
* *
2848706 TCACTAACGTTATCGATTTATAACAAAATAC
1 TCACTAACGTTATCGATTTGTAACAAAATAA
2848737 TCACT
1 TCACT
2848742 CCACCGTTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (31 bp):
TCACTAACGTTATCGATTTGTAACAAAATAA
Found at i:2852054 original size:19 final size:19
Alignment explanation
Indices: 2852030--2852069 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2852020 AAATGTAATG
2852030 AAGATAAAAAATAAAAATA
1 AAGATAAAAAATAAAAATA
**
2852049 AAGATAAGGAATAAAAATA
1 AAGATAAAAAATAAAAATA
2852068 AA
1 AA
2852070 AATGAAATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (19 bp):
AAGATAAAAAATAAAAATA
Found at i:2852083 original size:25 final size:23
Alignment explanation
Indices: 2852035--2852094 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 23
2852025 TAATGAAGAT
2852035 AAAAAATAAAAATAAAGATAAGG
1 AAAAAATAAAAATAAAGATAAGG
* *
2852058 AATAAAAATAAAAATGAA-ATGGAGG
1 -A-AAAAATAAAAATAAAGAT-AAGG
2852083 AAAAAATAAAAA
1 AAAAAATAAAAA
2852095 GGGTAAATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 11 0.34
24 4 0.12
25 17 0.53
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (23 bp):
AAAAAATAAAAATAAAGATAAGG
Found at i:2852126 original size:3 final size:3
Alignment explanation
Indices: 2852110--2852160 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
2852100 AATAGAAATA
2852110 AAT AA- AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2852156 AAT AA
1 AAT AA
2852161 AAGCAGTAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2852448 original size:17 final size:17
Alignment explanation
Indices: 2852426--2852509 Score: 57
Period size: 17 Copynumber: 4.9 Consensus size: 17
2852416 ATAAAATGTT
2852426 TTAAAAATAATAATAAA
1 TTAAAAATAATAATAAA
* *
2852443 TTAAAAAAAGATAAAAAA
1 TTAAAAATA-ATAATAAA
*
2852461 ATAAAACAT-AT-A-AAA
1 TTAAAA-ATAATAATAAA
*
2852476 TATAATAATAATAATAAA
1 T-TAAAAATAATAATAAA
* * *
2852494 GTATATATAATAATAA
1 TTAAAAATAATAATAA
2852510 TAATAGTAAG
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
15 5 0.10
16 7 0.14
17 23 0.45
18 15 0.29
19 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.27
Consensus pattern (17 bp):
TTAAAAATAATAATAAA
Found at i:2852931 original size:37 final size:37
Alignment explanation
Indices: 2852881--2852992 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
2852871 ATGCTTATAG
* *
2852881 ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAACTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
2852918 ATCCTATTTTTAGGAGTTTAAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
2852955 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
2852992 A
1 A
2852993 ACGTTATGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:2853848 original size:34 final size:34
Alignment explanation
Indices: 2853782--2854037 Score: 132
Period size: 34 Copynumber: 7.4 Consensus size: 34
2853772 TATTGGTGTT
* *
2853782 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTC
1 TCAAGAGAGAC--AAC-TTGTTTAAAGAGAAACTGTC
*
2853819 TCAATAGAGACAACTTGTTTAAAGAGAAACTGTC
1 TCAAGAGAGACAACTTGTTTAAAGAGAAACTGTC
**
2853853 TCAAGAGAGACAAAACTTAGTTCCGAA-AGAAACTGTC
1 TCAAGAGAGAC--AACTT-GTT-TAAAGAGAAACTGTC
* * * * *
2853890 TCAAGGGAGACAAAATTTGCTTCAAG-GAAAACATAT-
1 TCAAGAGAGAC--AACTTGTTTAAAGAG-AAAC-TGTC
* ** * *
2853926 T-TA-A-AG--ATTTTGTTTCAAGGGAAACTGTC
1 TCAAGAGAGACAACTTGTTTAAAGAGAAACTGTC
* * * *
2853955 TCAAGAGAGATAATTTGTTTTAAGGGAAACTGTC
1 TCAAGAGAGACAACTTGTTTAAAGAGAAACTGTC
* * *
2853989 TCAAGAGAGACAAATTTTGTTTCAAGGGAAACTGTC
1 TCAAGAGAGAC-AA-CTTGTTTAAAGAGAAACTGTC
*
2854025 CCAAGAGAGACAA
1 TCAAGAGAGACAA
2854038 AATTTGTTTC
Statistics
Matches: 180, Mismatches: 23, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
28 2 0.01
29 16 0.09
30 2 0.01
31 1 0.01
32 2 0.01
33 2 0.01
34 59 0.33
35 11 0.06
36 42 0.23
37 41 0.23
38 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (34 bp):
TCAAGAGAGACAACTTGTTTAAAGAGAAACTGTC
Found at i:2853860 original size:15 final size:15
Alignment explanation
Indices: 2853804--2853860 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
2853794 AAACTTTGTT
*
2853804 TCAAGGGAAACTGTC
1 TCAAGAGAAACTGTC
*
2853819 TCAATAGAGACAACTTGTT
1 TC-A-AGAGA-AAC-TGTC
*
2853838 TAAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
2853853 TCAAGAGA
1 TCAAGAGA
2853861 GACAAAACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 12 0.36
16 4 0.12
17 9 0.27
18 4 0.12
19 4 0.12
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:2854008 original size:36 final size:36
Alignment explanation
Indices: 2853932--2854050 Score: 188
Period size: 36 Copynumber: 3.4 Consensus size: 36
2853922 ATATTTAAAG
*
2853932 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA-TA
1 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
2853967 A-TTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAA
1 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
2854002 ATTTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAA
1 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
2854038 AATTTGTTTCAAG
1 ATTTTGTTTCAAG
2854051 AGAGACAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
34 30 0.39
35 3 0.04
36 44 0.57
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (36 bp):
ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:2854052 original size:21 final size:22
Alignment explanation
Indices: 2854026--2854068 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
2854016 GAAACTGTCC
2854026 CAAGAGAGACAAAA-TTTGTTT
1 CAAGAGAGACAAAACTTTGTTT
2854047 CAAGAGAGACAAAACTTTGTTT
1 CAAGAGAGACAAAACTTTGTTT
2854069 TGAGTAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (22 bp):
CAAGAGAGACAAAACTTTGTTT
Found at i:2854601 original size:43 final size:43
Alignment explanation
Indices: 2854554--2854651 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
2854544 TTCTTTGTGA
**
2854554 AGTTGAAATCGTGG-TT-GTATGGGCACGATATCCTTTATCGTGG
1 AGTTGAAATCGTGGATTCG--TGGGCACGATATCCTCCATCGTGG
*
2854597 AGTTGAAATCGTGGATTCGTGGGTACGATATCCTCCATCGTGG
1 AGTTGAAATCGTGGATTCGTGGGCACGATATCCTCCATCGTGG
2854640 AGTTGAAATCGT
1 AGTTGAAATCGT
2854652 TAATGACCCA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
43 47 0.94
44 2 0.04
45 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (43 bp):
AGTTGAAATCGTGGATTCGTGGGCACGATATCCTCCATCGTGG
Found at i:2854765 original size:87 final size:87
Alignment explanation
Indices: 2854662--2854851 Score: 371
Period size: 87 Copynumber: 2.2 Consensus size: 87
2854652 TAATGACCCA
*
2854662 TTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGTATTGAA
1 TTCGTCGTGAAGTTGAGCCTTGACTTAAATATCCTTCGTCGTGAAGTTGAAATCCAAGTATTGAA
2854727 TGTTGTTTGGAGTTGAATATCC
66 TGTTGTTTGGAGTTGAATATCC
2854749 TTCGTCGTGAAGTTGAGCCTTGACTTAAATATCCTTCGTCGTGAAGTTGAAATCCAAGTATTGAA
1 TTCGTCGTGAAGTTGAGCCTTGACTTAAATATCCTTCGTCGTGAAGTTGAAATCCAAGTATTGAA
2854814 TGTTGTTTGGAGTTGAATATCC
66 TGTTGTTTGGAGTTGAATATCC
2854836 TTCGTCGTGAAGTTGA
1 TTCGTCGTGAAGTTGA
2854852 AATTCAATCT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 102 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (87 bp):
TTCGTCGTGAAGTTGAGCCTTGACTTAAATATCCTTCGTCGTGAAGTTGAAATCCAAGTATTGAA
TGTTGTTTGGAGTTGAATATCC
Found at i:2856342 original size:14 final size:13
Alignment explanation
Indices: 2856319--2856380 Score: 63
Period size: 13 Copynumber: 4.7 Consensus size: 13
2856309 TTTTCCTTTG
*
2856319 TTTTTGTTTCTCT
1 TTTTTTTTTCTCT
2856332 TTTTTATTTTCTCT
1 TTTTT-TTTTCTCT
* *
2856346 ATGTTTTTTCT-T
1 TTTTTTTTTCTCT
*
2856358 TGTTTTTTTCTCT
1 TTTTTTTTTCTCT
2856371 TTTTTGTTTT
1 TTTTT-TTTT
2856381 TGTTCAAATC
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
12 9 0.23
13 16 0.41
14 14 0.36
ACGTcount: A:0.03, C:0.11, G:0.06, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCTCT
Found at i:2859616 original size:15 final size:15
Alignment explanation
Indices: 2859579--2859628 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
2859569 TAAAAAGGGT
*
2859579 AAATAGAAATAA-ATA
1 AAATAAAAATAATA-A
2859594 AAAT-AAAATAATAA
1 AAATAAAAATAATAA
*
2859608 AAATAAAAATACTAA
1 AAATAAAAATAATAA
*
2859623 TAATAA
1 AAATAA
2859629 TAAAAATAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
AAATAAAAATAATAA
Found at i:2859625 original size:18 final size:18
Alignment explanation
Indices: 2859602--2859636 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2859592 TAAAATAAAA
2859602 TAATAAAAATAAAAATAC
1 TAATAAAAATAAAAATAC
*
2859620 TAATAATAATAAAAATA
1 TAATAAAAATAAAAATA
2859637 GTAAGTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
TAATAAAAATAAAAATAC
Found at i:2859995 original size:26 final size:26
Alignment explanation
Indices: 2859886--2859995 Score: 68
Period size: 26 Copynumber: 4.2 Consensus size: 26
2859876 AAAATGTTTT
2859886 AAATAATAATAATAAT-AAATTAAAA-A
1 AAATAATAATAATAATGAAA--AAAATA
* *
2859912 AAGATAA-AACAA-AAT-AAAACATATAA
1 AA-ATAATAATAATAATGAAAA-AAAT-A
** *
2859938 AACATAATAATAATAATGAAGTATATA
1 AA-ATAATAATAATAATGAAAAAAATA
* *
2859965 TAATAATAATAGTAATGAAAAAAATA
1 AAATAATAATAATAATGAAAAAAATA
2859991 AAATA
1 AAATA
2859996 TAAAAAAATT
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
23 1 0.02
24 2 0.03
25 6 0.09
26 37 0.57
27 10 0.15
28 7 0.11
29 2 0.03
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (26 bp):
AAATAATAATAATAATGAAAAAAATA
Found at i:2860384 original size:37 final size:37
Alignment explanation
Indices: 2860334--2860445 Score: 197
Period size: 37 Copynumber: 3.0 Consensus size: 37
2860324 ATGCTTATGG
*
2860334 ATCATATTTTTAGGAGTTTGAATCTTAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
2860371 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* *
2860408 ATCATATTTTTAGAAGTTTGAATCCTAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
2860445 A
1 A
2860446 ACGTTATGTT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:2860661 original size:20 final size:20
Alignment explanation
Indices: 2860591--2860663 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
2860581 TTGGGCTGGG
* *
2860591 AGTATCGATACTCGTTTATGT
1 AGTATCGATACTC-TTAATGA
* * *
2860612 GGTATTGATACTATTCAAT-A
1 AGTATCGATACTCTT-AATGA
* *
2860632 AGTATTGATACTCTTAATGC
1 AGTATCGATACTCTTAATGA
2860652 AGTATCGATACT
1 AGTATCGATACT
2860664 TGCGTAGCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.07
20 26 0.63
21 12 0.29
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (20 bp):
AGTATCGATACTCTTAATGA
Found at i:2864336 original size:2 final size:2
Alignment explanation
Indices: 2864329--2864364 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2864319 AAAACTACAC
2864329 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2864365 GACACACACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2864945 original size:19 final size:20
Alignment explanation
Indices: 2864918--2864956 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2864908 AAATGCCCTT
*
2864918 AAAT-TTTTTTTTCTTTCAA
1 AAATATTTTTATTCTTTCAA
2864937 AAATATTTTTATTCTTTCAA
1 AAATATTTTTATTCTTTCAA
2864957 GAAAAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (20 bp):
AAATATTTTTATTCTTTCAA
Found at i:2865403 original size:20 final size:20
Alignment explanation
Indices: 2865359--2865406 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2865349 CTATTCCCTG
* *
2865359 ATAATCTTTTATTCTCACTG
1 ATAATCTTTTATTCCCACTA
*
2865379 GTAATCTTTTATTCCCACTA
1 ATAATCTTTTATTCCCACTA
2865399 ATAATCTT
1 ATAATCTT
2865407 ACATTTTGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.21, G:0.04, T:0.48
Consensus pattern (20 bp):
ATAATCTTTTATTCCCACTA
Found at i:2870857 original size:31 final size:31
Alignment explanation
Indices: 2870820--2870889 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 31
2870810 TGACACACAC
*
2870820 TAATTCTTTTTTTGGAATAAGTATCACACGT
1 TAATTCTTTTTTTGAAATAAGTATCACACGT
* *
2870851 TTATTC-TTTTTTGAAATAAGTATCACATGT
1 TAATTCTTTTTTTGAAATAAGTATCACACGT
2870881 TAATTCTTT
1 TAATTCTTT
2870890 AAATGTGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 27 0.79
31 7 0.21
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.50
Consensus pattern (31 bp):
TAATTCTTTTTTTGAAATAAGTATCACACGT
Found at i:2877873 original size:31 final size:31
Alignment explanation
Indices: 2877835--2877928 Score: 163
Period size: 31 Copynumber: 3.0 Consensus size: 31
2877825 CCCGAAAGAC
*
2877835 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
2877866 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2877897 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2877928 C
1 C
2877929 CCTCGACCCT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2878718 original size:64 final size:64
Alignment explanation
Indices: 2878584--2878743 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 64
2878574 GTAATGAAGG
* * ***
2878584 TATGCATCGATGCACTACTGATGCATCGGTACATAAAATGCATTCGATGTTGTATTATTACTGG
1 TATGCATCGATGCACTACTTATGCATCGATACATAAAATGCATTCGATGTTGTATTATTACAAA
* * * *
2878648 TATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTA-AAA
1 TATGCATCGATGCACTACTTATGCATCGATACATAAAATGCATTCGATG-TTGTATTATTACAAA
* * * *
2878711 TAGTGCATTGATGCACTTCCTGTGCATCGATAC
1 TA-TGCATCGATGCACTACTTATGCATCGATAC
2878744 GCCTTCAAAC
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
63 2 0.03
64 72 0.90
65 6 0.08
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (64 bp):
TATGCATCGATGCACTACTTATGCATCGATACATAAAATGCATTCGATGTTGTATTATTACAAA
Found at i:2883883 original size:21 final size:21
Alignment explanation
Indices: 2883859--2883919 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2883849 AACTTTGAAA
2883859 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
2883880 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
2883894 AAATAGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
2883915 AAATG
1 AAATG
2883920 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:2883965 original size:36 final size:36
Alignment explanation
Indices: 2883851--2883969 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
2883841 TGGTAACCAA
*
2883851 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
2883888 CTTTG-AAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
2883923 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
2883960 -GTTGAAAAAT
1 CTTTGAAAAAT
2883970 GATAATGGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
35 34 0.44
36 16 0.21
37 27 0.35
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2884368 original size:12 final size:12
Alignment explanation
Indices: 2884351--2884375 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2884341 ATTTTTTGCG
2884351 AGGTTACTATTC
1 AGGTTACTATTC
2884363 AGGTTACTATTC
1 AGGTTACTATTC
2884375 A
1 A
2884376 CATGAATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGGTTACTATTC
Found at i:2888570 original size:37 final size:37
Alignment explanation
Indices: 2888471--2888589 Score: 165
Period size: 35 Copynumber: 3.3 Consensus size: 37
2888461 TGGTAACCAA
*
2888471 CTTTGAAAAA-ATGGTTTTCAAAATTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
2888508 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
2888543 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
2888580 -GTTGAAAAAT
1 CTTTGAAAAAT
2888590 GATAATGGGA
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
35 29 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2891774 original size:18 final size:19
Alignment explanation
Indices: 2891751--2891795 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
2891741 CTCAGTAATC
2891751 ATATTCC-CTGGTAATCTT
1 ATATTCCACTGGTAATCTT
*
2891769 ATATTCCTACTGGTAGTCTT
1 ATATTCC-ACTGGTAATCTT
*
2891789 ACATTCC
1 ATATTCC
2891796 GAGAACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42
Consensus pattern (19 bp):
ATATTCCACTGGTAATCTT
Found at i:2891783 original size:20 final size:20
Alignment explanation
Indices: 2891758--2891795 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2891748 ATCATATTCC
*
2891758 CTGGTAATCTTATATTCCTA
1 CTGGTAATCTTACATTCCTA
*
2891778 CTGGTAGTCTTACATTCC
1 CTGGTAATCTTACATTCC
2891796 GAGAACCAAA
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:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:2892125 original size:41 final size:41
Alignment explanation
Indices: 2892088--2892175 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
2892078 CTATCGCATT
* * *
2892088 GCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAAC
1 GCGAATTTCCAAAATCGCAATGCGAATACGTAAATCGCAAC
** *
2892129 GCGAATTTGGAAAATCGCAATGCGATTACGTAAATCGCAAC
1 GCGAATTTCCAAAATCGCAATGCGAATACGTAAATCGCAAC
2892170 GCGAAT
1 GCGAAT
2892176 ACGTAAATCG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (41 bp):
GCGAATTTCCAAAATCGCAATGCGAATACGTAAATCGCAAC
Found at i:2892126 original size:61 final size:61
Alignment explanation
Indices: 2892061--2892218 Score: 212
Period size: 61 Copynumber: 2.6 Consensus size: 61
2892051 GTTACCAGAT
* * * *
2892061 TCGCAACGCGATTCTGACTATCGCATTGCGATTTTCCTAATTCGCAATGCGAATACGTAAA
1 TCGCAACGCGATTCTGACTATCGCAATGCGATTTACCTAAATCGCAACGCGAATACGTAAA
** *
2892122 TCGCAACGCGAATT-TGGAAAATCGCAATGCGA-TTACGTAAATCGCAACGCGAATACGTAAA
1 TCGCAACGCG-ATTCT-GACTATCGCAATGCGATTTACCTAAATCGCAACGCGAATACGTAAA
*
2892183 TCGCAACGCGAATCTGACTATCGCAATGCGATTTAC
1 TCGCAACGCGATTCTGACTATCGCAATGCGATTTAC
2892219 ATAGCGCTAT
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
60 16 0.19
61 51 0.61
62 16 0.19
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (61 bp):
TCGCAACGCGATTCTGACTATCGCAATGCGATTTACCTAAATCGCAACGCGAATACGTAAA
Found at i:2892127 original size:20 final size:20
Alignment explanation
Indices: 2892102--2892195 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
2892092 TTTTCCTAAT
*
2892102 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
** *
2892122 TCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGAA-TACGTAAA
* *
2892143 TCGCAATGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
2892163 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
2892183 TCGCAACGCGAAT
1 TCGCAACGCGAAT
2892196 CTGACTATCG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:2892417 original size:22 final size:22
Alignment explanation
Indices: 2892392--2892457 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
2892382 GGCGACATCC
2892392 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
2892414 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
*
2892436 GTCTCCATCTCC-AGCGAAATCA
1 GTCCCCATCTCCGA-CGAAATCA
2892458 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 1 0.03
22 39 0.98
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:2892866 original size:20 final size:20
Alignment explanation
Indices: 2892793--2892883 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
2892783 GCGATTCTGT
2892793 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
* ** **
2892812 CATTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
2892832 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
2892852 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
2892872 TGTTGCGATTTT
1 CGTTGCGATTTT
2892884 AAGTTTCAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 11 0.18
20 50 0.82
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:2892890 original size:20 final size:20
Alignment explanation
Indices: 2892847--2892890 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2892837 CGATAGTCAT
* *
2892847 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
2892867 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
2892887 TTTC
1 TTTC
2892891 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:2894784 original size:20 final size:20
Alignment explanation
Indices: 2894759--2894900 Score: 114
Period size: 20 Copynumber: 7.8 Consensus size: 20
2894749 AGAATAGTTT
2894759 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2894779 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2894799 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
2894815 A--ATCGTAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
2894832 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
2894848 A--ATCGCAAAGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2894866 ATTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
2894886 ACTATCGCAATGCGA
1 ACTATCGCAATGCGA
2894901 CTATCACAAT
Statistics
Matches: 101, Mismatches: 7, Indels: 28
0.74 0.05 0.21
Matches are distributed among these distances:
14 13 0.13
16 10 0.10
17 8 0.08
18 5 0.05
19 6 0.06
20 59 0.58
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:2894904 original size:14 final size:14
Alignment explanation
Indices: 2894885--2894914 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2894875 ATGCGAAAAT
*
2894885 GACTATCGCAATGC
1 GACTATCACAATGC
2894899 GACTATCACAATGC
1 GACTATCACAATGC
2894913 GA
1 GA
2894915 ATTTGACTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (14 bp):
GACTATCACAATGC
Found at i:2895001 original size:20 final size:20
Alignment explanation
Indices: 2894976--2895062 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
2894966 GATTCTCTCG
*
2894976 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAATTTCGCA
2894996 TTGCGATAGT-AATTTTCGCA
1 TTGCGATAGTCAA-TTTCGCA
* *
2895016 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAATTTCGCA
* *
2895036 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAATTTCGCA
2895056 TTGCGAT
1 TTGCGAT
2895063 TTTAAGTTTC
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
19 2 0.03
20 59 0.95
21 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAATTTCGCA
Found at i:2895034 original size:40 final size:40
Alignment explanation
Indices: 2894976--2895062 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 40
2894966 GATTCTCTCG
2894976 TTGCGATAGTCAAATTCGCATTGCGATAGTAATTTTCGCA
1 TTGCGATAGTCAAATTCGCATTGCGATAGTAATTTTCGCA
** * * *
2895016 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCATTGCGATAGTAATTTTCGCA
2895056 TTGCGAT
1 TTGCGAT
2895063 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (40 bp):
TTGCGATAGTCAAATTCGCATTGCGATAGTAATTTTCGCA
Found at i:2895072 original size:20 final size:20
Alignment explanation
Indices: 2894974--2895072 Score: 92
Period size: 20 Copynumber: 5.0 Consensus size: 20
2894964 GTGATTCTCT
*
2894974 CGTTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
* *
2894994 CATTGCGATAGTAATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* * *
2895014 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* *
2895034 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
2895054 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATAGTAAGTTTC
2895073 AGATTCTATT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
19 2 0.03
20 68 0.97
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:2895587 original size:18 final size:19
Alignment explanation
Indices: 2895549--2895589 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
2895539 TTACCTGTCG
2895549 TCGTTCAAGAGGCCTCCCCTA
1 TCGTTCAAGAGG-C-CCCCTA
2895570 TCGTTCAAGAGG-CCCCTA
1 TCGTTCAAGAGGCCCCCTA
2895588 TC
1 TC
2895590 ATCCCTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
21 12 0.60
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.24
Consensus pattern (19 bp):
TCGTTCAAGAGGCCCCCTA
Found at i:2897066 original size:14 final size:14
Alignment explanation
Indices: 2897032--2897070 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2897022 TTGATTGTTT
2897032 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
2897046 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
2897060 TGTTGATTTGT
1 AATTGATTTGT
2897071 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2897298 original size:34 final size:34
Alignment explanation
Indices: 2897253--2897348 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
2897243 ATTAGTTTCG
*
2897253 CGTTGCAATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
2897287 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
2897320 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
2897349 AGTCAATTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:2897345 original size:20 final size:20
Alignment explanation
Indices: 2897320--2897408 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
2897310 GCGATTCTCT
2897320 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
2897340 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
2897360 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
2897380 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
2897400 CGTTGCGAT
1 CGTTGCGAT
2897409 TTCTGCGTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:2899875 original size:24 final size:24
Alignment explanation
Indices: 2899841--2899894 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2899831 CTGAAACATC
2899841 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2899865 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2899889 ATCAAA
1 ATCAAA
2899895 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2900797 original size:20 final size:20
Alignment explanation
Indices: 2900735--2900788 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
2900725 AAATTCAGTA
2900735 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
2900755 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
2900775 TTGCGATAGTCAGA
1 TTGCGATAGTCAGA
2900789 TTTGCGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:2900808 original size:20 final size:20
Alignment explanation
Indices: 2900785--2900901 Score: 87
Period size: 20 Copynumber: 5.8 Consensus size: 20
2900775 TTGCGATAGT
* *
2900785 CAGATTTGCGTTGTGATTTA
1 CAGATTCGCGTTGCGATTTA
2900805 CAGATTCGCGTTGCGATTTA
1 CAGATTCGCGTTGCGATTTA
*
2900825 C-GTATTCGCATTGCGATTTA
1 CAG-ATTCGCGTTGCGATTTA
* ** * *
2900845 C-GTAATCGTATTACGATTTTT
1 CAG-ATTCGCGTTGCGA-TTTA
*
2900866 CAAATTCGCGTTGCGATTTA
1 CAGATTCGCGTTGCGATTTA
*
2900886 C-GTATTCGCATTGCGA
1 CAG-ATTCGCGTTGCGA
2900902 ATTAGGAAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.01
20 64 0.82
21 13 0.17
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
CAGATTCGCGTTGCGATTTA
Found at i:2900922 original size:21 final size:21
Alignment explanation
Indices: 2900898--2900943 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2900888 TATTCGCATT
*
2900898 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGAAAAATCGCAAC
* *
2900919 GCGAATTTGAAAAATCGCAAT
1 GCGAATTAGAAAAATCGCAAC
2900940 GCGA
1 GCGA
2900944 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGAAAAATCGCAAC
Found at i:2904876 original size:22 final size:22
Alignment explanation
Indices: 2904837--2904878 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2904827 TAATCGACTG
*
2904837 AATTAACCGACTAAATTAATCA
1 AATTAACCGACAAAATTAATCA
2904859 AATTAACCGA-AAATATTAAT
1 AATTAACCGACAAA-ATTAAT
2904879 TATTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (22 bp):
AATTAACCGACAAAATTAATCA
Found at i:2906671 original size:29 final size:27
Alignment explanation
Indices: 2906599--2906680 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 27
2906589 ATATAACATT
*
2906599 ATATATAAACTAATTAGACAAGTGAAA
1 ATATATAAAATAATTAGACAAGTGAAA
* *
2906626 AT-TATATAA-AACTAGACAAGTGAAA
1 ATATATAAAATAATTAGACAAGTGAAA
*
2906651 ATCATATAAAATTAATTAGACTAGTGAAA
1 AT-ATATAAAA-TAATTAGACAAGTGAAA
2906680 A
1 A
2906681 CAGACCATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
25 17 0.38
26 5 0.11
27 8 0.18
29 15 0.33
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (27 bp):
ATATATAAAATAATTAGACAAGTGAAA
Found at i:2906719 original size:20 final size:19
Alignment explanation
Indices: 2906696--2906741 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
2906686 CATAAGAAAT
*
2906696 AAAAATAATATTCATTAAAG
1 AAAAATAATATT-ATCAAAG
2906716 -AAAAT-AT-TTATCAAAG
1 AAAAATAATATTATCAAAG
2906732 AAAAATAATA
1 AAAAATAATA
2906742 AGATAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 4 0.18
19 5 0.23
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (19 bp):
AAAAATAATATTATCAAAG
Found at i:2906738 original size:17 final size:16
Alignment explanation
Indices: 2906702--2906735 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2906692 AAATAAAAAT
*
2906702 AATATTCATTAAAGAA
1 AATATTCATCAAAGAA
*
2906718 AATATTTATCAAAGAA
1 AATATTCATCAAAGAA
2906734 AA
1 AA
2906736 ATAATAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
AATATTCATCAAAGAA
Found at i:2909460 original size:23 final size:23
Alignment explanation
Indices: 2909433--2909534 Score: 107
Period size: 23 Copynumber: 4.4 Consensus size: 23
2909423 AGAGTCAGGG
* *
2909433 TTCTACGTGGTCCTTCAGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
2909456 TTCTATGTGGTCCTTCGGGA-AA
1 TTCTATGTGGTCCTTCGGGACAA
* * *
2909478 TTTCTACGTAGTTCTTCGGGACAA
1 -TTCTATGTGGTCCTTCGGGACAA
* * * *
2909502 TACTATATGGTCCTTTGGGACAT
1 TTCTATGTGGTCCTTCGGGACAA
2909525 TTCTATGTGG
1 TTCTATGTGG
2909535 CACTTCAGTG
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
22 2 0.03
23 59 0.94
24 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAA
Found at i:2909500 original size:46 final size:46
Alignment explanation
Indices: 2909433--2909529 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 46
2909423 AGAGTCAGGG
* * *
2909433 TTCTACGTGGTCCTTCAGGACAATTCTATGTGGTCCTTCGGGAAAT
1 TTCTACGTAGTCCTTCAGGACAATACTATATGGTCCTTCGGGAAAT
* * * *
2909479 TTCTACGTAGTTCTTCGGGACAATACTATATGGTCCTTTGGGACAT
1 TTCTACGTAGTCCTTCAGGACAATACTATATGGTCCTTCGGGAAAT
2909525 TTCTA
1 TTCTA
2909530 TGTGGCACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (46 bp):
TTCTACGTAGTCCTTCAGGACAATACTATATGGTCCTTCGGGAAAT
Found at i:2909560 original size:24 final size:24
Alignment explanation
Indices: 2909533--2909579 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2909523 ATTTCTATGT
2909533 GGCACTTCAG-TGCAATTTATACGC
1 GGCACTT-AGATGCAATTTATACGC
*
2909557 GGCACTTTGATGCAATTTATACG
1 GGCACTTAGATGCAATTTATACG
2909580 AGTTGTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (24 bp):
GGCACTTAGATGCAATTTATACGC
Found at i:2915360 original size:37 final size:35
Alignment explanation
Indices: 2915302--2915373 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 35
2915292 ATGCATAAGT
2915302 TTATATGTTATATGCATTGTTATGCATGAGCTATGTG
1 TTATATGTTATATGCATTGTTAT--ATGAGCTATGTG
*
2915339 TTATATGTTAT-T-CTATATGTTATATGATCTATGTG
1 TTATATGTTATATGC-AT-TGTTATATGAGCTATGTG
2915374 AATATATGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
35 12 0.38
36 3 0.09
37 17 0.53
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.50
Consensus pattern (35 bp):
TTATATGTTATATGCATTGTTATATGAGCTATGTG
Found at i:2918889 original size:3 final size:3
Alignment explanation
Indices: 2918881--2918917 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2918871 TTAAATTAAG
2918881 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2918918 ATAATATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2921578 original size:19 final size:19
Alignment explanation
Indices: 2921551--2921607 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
2921541 AAGCTAATAG
2921551 GCTGAAAGCACTAGAAAGA
1 GCTGAAAGCACTAGAAAGA
* *
2921570 GCTGCAAG--CTA-ATAG-
1 GCTGAAAGCACTAGAAAGA
2921585 GCTGAAAGCACTAGAAAGA
1 GCTGAAAGCACTAGAAAGA
2921604 GCTG
1 GCTG
2921608 CAGCCAGAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 7 0.23
16 3 0.10
17 6 0.20
18 3 0.10
19 11 0.37
ACGTcount: A:0.40, C:0.18, G:0.28, T:0.14
Consensus pattern (19 bp):
GCTGAAAGCACTAGAAAGA
Found at i:2921584 original size:34 final size:34
Alignment explanation
Indices: 2921541--2921609 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
2921531 GCTCGCATGG
2921541 AAGCTAATAGGCTGAAAGCACTAGAAAGAGCTGC
1 AAGCTAATAGGCTGAAAGCACTAGAAAGAGCTGC
2921575 AAGCTAATAGGCTGAAAGCACTAGAAAGAGCTGC
1 AAGCTAATAGGCTGAAAGCACTAGAAAGAGCTGC
2921609 A
1 A
2921610 GCCAGAGCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.17, G:0.26, T:0.14
Consensus pattern (34 bp):
AAGCTAATAGGCTGAAAGCACTAGAAAGAGCTGC
Found at i:2921593 original size:15 final size:15
Alignment explanation
Indices: 2921541--2921593 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
2921531 GCTCGCATGG
2921541 AAGCTAATAGGCTGA
1 AAGCTAATAGGCTGA
* *
2921556 AAGCACTAGAAAGAGCTGC
1 AAG--CTA-ATAG-GCTGA
2921575 AAGCTAATAGGCTGA
1 AAGCTAATAGGCTGA
2921590 AAGC
1 AAGC
2921594 ACTAGAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 11 0.37
16 3 0.10
17 6 0.20
18 3 0.10
19 7 0.23
ACGTcount: A:0.42, C:0.17, G:0.26, T:0.15
Consensus pattern (15 bp):
AAGCTAATAGGCTGA
Found at i:2928836 original size:26 final size:25
Alignment explanation
Indices: 2928788--2928843 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
2928778 ATTTGATGAT
* *
2928788 TTATTTAATTTTTTAAAATAAATTA
1 TTATTTAATATTTTAAAATAAATAA
2928813 TTATTTAA-ATTTTAAAATAAAAATAA
1 TTATTTAATATTTTAAAAT--AAATAA
2928839 TTATT
1 TTATT
2928844 AAGATATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 9 0.33
25 8 0.30
26 10 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATTTAATATTTTAAAATAAATAA
Found at i:2933964 original size:188 final size:184
Alignment explanation
Indices: 2933649--2934040 Score: 669
Period size: 188 Copynumber: 2.1 Consensus size: 184
2933639 ATAAAATTTT
* **
2933649 AAATATTAAATATATTATATATATCATATGGGCTCAGCCCAAACCATTTAAAATTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
2933714 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
*
2933779 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTCTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTT-T-AATTAAA
2933835 AAATATTAAATATATAATATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAAT
1 AAATATTAAATATAT--TATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAAT
2933900 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAAT
64 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAAT
* *
2933965 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTATA
129 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTAATTAAA
* *
2934021 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
2934041 AATTAGAAAA
Statistics
Matches: 196, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
183 6 0.03
185 2 0.01
186 31 0.16
187 1 0.01
188 156 0.80
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTAATTAAA
Found at i:2936485 original size:15 final size:18
Alignment explanation
Indices: 2936451--2936489 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 18
2936441 AATTTATGTC
2936451 AATTTTATTGATTAATTT
1 AATTTTATTGATTAATTT
2936469 AATTTT-TT-ATT-ATTT
1 AATTTTATTGATTAATTT
2936484 AATTTT
1 AATTTT
2936490 GTTTAACCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 3 0.14
17 2 0.10
18 6 0.29
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
AATTTTATTGATTAATTT
Found at i:2942200 original size:5 final size:5
Alignment explanation
Indices: 2942190--2942269 Score: 69
Period size: 5 Copynumber: 15.8 Consensus size: 5
2942180 AATTATTTTT
*
2942190 TATTA TATTA TATTA TATTTA TTTTA TATT- TAATTA T-TTGA -ATTA
1 TATTA TATTA TATTA TA-TTA TATTA TATTA T-ATTA TATT-A TATTA
*
2942235 TTTTA TATT- TAATTA TATTA TATTTA TATTA TATT
1 TATTA TATTA T-ATTA TATTA TA-TTA TATTA TATT
2942270 TAATTATTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
4 5 0.08
5 46 0.74
6 11 0.18
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (5 bp):
TATTA
Found at i:2942235 original size:9 final size:8
Alignment explanation
Indices: 2942216--2942278 Score: 51
Period size: 8 Copynumber: 7.6 Consensus size: 8
2942206 ATTTATTTTA
2942216 TATTTAAT
1 TATTTAAT
2942224 TATTTGAAT
1 TATTT-AAT
*
2942233 TATTTTA-
1 TATTTAAT
2942240 TATTTAAT
1 TATTTAAT
2942248 TATATT-A-
1 TAT-TTAAT
2942255 TATTTATATT
1 TATTTA-A-T
2942265 ATATTTAAT
1 -TATTTAAT
2942274 TATTT
1 TATTT
2942279 TTTGAATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
6 2 0.04
7 9 0.20
8 16 0.36
9 11 0.24
10 1 0.02
11 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (8 bp):
TATTTAAT
Found at i:2942250 original size:50 final size:50
Alignment explanation
Indices: 2942180--2942278 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
2942170 TAGAAGGTAA
* *
2942180 AATTATTTTTTATTATATTATATTATATTTATTTTATATTTAATTATTTG
1 AATTATTTTATATTATATTATATTATATTTATATTATATTTAATTATTTG
2942230 AATTATTTTATATT-TAATTATATTATATTTATATTATATTTAATTATTT
1 AATTATTTTATATTAT-ATTATATTATATTTATATTATATTTAATTATTT
2942279 TTTGAATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 1 0.02
50 45 0.98
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (50 bp):
AATTATTTTATATTATATTATATTATATTTATATTATATTTAATTATTTG
Found at i:2945572 original size:14 final size:13
Alignment explanation
Indices: 2945555--2945590 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2945545 TAAACTAAAT
*
2945555 AATAAAAACAATTA
1 AATACAAAC-ATTA
2945569 AATACAAACATTA
1 AATACAAACATTA
2945582 AATACAAAC
1 AATACAAAC
2945591 TATACAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (13 bp):
AATACAAACATTA
Found at i:2945583 original size:13 final size:14
Alignment explanation
Indices: 2945555--2945613 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
2945545 TAAACTAAAT
*
2945555 AATAAAAACAATTA
1 AATACAAACAATTA
2945569 AATACAAAC-ATTA
1 AATACAAACAATTA
*
2945582 AATACAAACTA-TA
1 AATACAAACAATTA
* *
2945595 CAATTCAAACAAATA
1 -AATACAAACAATTA
2945610 AATA
1 AATA
2945614 ATAAAAACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
13 15 0.39
14 21 0.55
15 2 0.05
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.22
Consensus pattern (14 bp):
AATACAAACAATTA
Found at i:2946151 original size:42 final size:42
Alignment explanation
Indices: 2946104--2946185 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
2946094 CCCTGCGGCA
** * *
2946104 GTGGCATTTGAA-CCAGTTATGGTGGCATCTGAAATGGTTGCG
1 GTGGCATTT-AACCCAACTATGATGGCATCTGAAACGGTTGCG
*
2946146 GTGGCATTTAACCCAACTATGATGGCATGTGAAACGGTTG
1 GTGGCATTTAACCCAACTATGATGGCATCTGAAACGGTTG
2946186 TGGAATATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.29
Consensus pattern (42 bp):
GTGGCATTTAACCCAACTATGATGGCATCTGAAACGGTTGCG
Found at i:2949397 original size:76 final size:76
Alignment explanation
Indices: 2949311--2949464 Score: 263
Period size: 76 Copynumber: 2.0 Consensus size: 76
2949301 AATGAATTTA
* *
2949311 ATACATATGAATAATCAAGTTACCATTTTATAATTTTTAATAATAAAATAACTCAATAAAATAAT
1 ATACATATGAATAATCAAATTACCATTTTATAACTTTTAATAATAAAATAACTCAATAAAATAAT
*
2949376 AATTTATAATT
66 AACTTATAATT
**
2949387 ATACATATGAATAATCAAATTATTATTTTATAACTTTTAATAATAAAATAACTCAATAAAATAAT
1 ATACATATGAATAATCAAATTACCATTTTATAACTTTTAATAATAAAATAACTCAATAAAATAAT
2949452 AACTTATAATT
66 AACTTATAATT
2949463 AT
1 AT
2949465 GAAATCATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (76 bp):
ATACATATGAATAATCAAATTACCATTTTATAACTTTTAATAATAAAATAACTCAATAAAATAAT
AACTTATAATT
Found at i:2954961 original size:45 final size:46
Alignment explanation
Indices: 2954912--2954998 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 46
2954902 GAACATCGAA
* * *
2954912 TGCATTTTATGCATCGATGCA-TATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
2954957 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCAC
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCAC
2954999 AAGACCATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
Found at i:2954990 original size:20 final size:20
Alignment explanation
Indices: 2954965--2955018 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2954955 AGTGCATTTG
2954965 ATGCATCGATGCACAAGACC
1 ATGCATCGATGCACAAGACC
2954985 ATGCATCGATGCACAAGACC
1 ATGCATCGATGCACAAGACC
*
2955005 ATGTATCGATGCAC
1 ATGCATCGATGCAC
2955019 TCAGGCTATT
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:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (20 bp):
ATGCATCGATGCACAAGACC
Found at i:2960914 original size:23 final size:22
Alignment explanation
Indices: 2960842--2960923 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 22
2960832 TCACTTAACA
2960842 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
** * *
2960866 GTGCATCGATTTA-TCTTG-CT
1 GTGCATCGATGCACCCTTGAAT
2960886 GATGCATCGATGCACGCCTTGAAT
1 G-TGCATCGATGCAC-CCTTGAAT
2960910 GTGCATCGATGCAC
1 GTGCATCGATGCAC
2960924 AGGGTCATGC
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
20 2 0.04
21 13 0.28
22 1 0.02
23 17 0.37
24 13 0.28
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:2963047 original size:20 final size:20
Alignment explanation
Indices: 2963009--2963047 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2962999 TTATTAATTT
*
2963009 TTGCATTATTGACATTTTAG
1 TTGCATTATTGACAATTTAG
2963029 TTGCATTA-TGACCAATTTA
1 TTGCATTATTGA-CAATTTA
2963048 CCATTTCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (20 bp):
TTGCATTATTGACAATTTAG
Found at i:2963685 original size:45 final size:46
Alignment explanation
Indices: 2963636--2963723 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 46
2963626 GAACATCGAA
* * *
2963636 TGCATTTTATGCATCGATGCAC-ATACCATACATCGATGCACTTAG
1 TGCATTTGATGCATCGATGAACAAGACCATACATCGATGCACTTAG
* *
2963681 TGCATTTGATGCATCGTTGAACAAGACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGAACAAGACCATACATCGATGCACT
2963724 CAGGCTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 19 0.51
46 18 0.49
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGAACAAGACCATACATCGATGCACTTAG
Found at i:2967116 original size:2 final size:2
Alignment explanation
Indices: 2967109--2967169 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
2967099 AGTATTTAAC
2967109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2967151 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2967170 CTTCGTAATC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2967499 original size:2 final size:2
Alignment explanation
Indices: 2967492--2967531 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2967482 GATAAAAGTA
2967492 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2967532 GAGACATTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2969146 original size:26 final size:27
Alignment explanation
Indices: 2969094--2969147 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
2969084 ACATGTGAGC
*
2969094 TAAATTAATTTTTTTCAAGTTCGAGGG
1 TAAATTAATTTTTTTCAAGTTCAAGGG
* *
2969121 TAAATT-ATTTTTTTTAAGTTTAAGGG
1 TAAATTAATTTTTTTCAAGTTCAAGGG
2969147 T
1 T
2969148 CTATTTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.50
Consensus pattern (27 bp):
TAAATTAATTTTTTTCAAGTTCAAGGG
Found at i:2970799 original size:20 final size:20
Alignment explanation
Indices: 2970774--2970866 Score: 114
Period size: 21 Copynumber: 4.5 Consensus size: 20
2970764 TTTTCCCAAT
2970774 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
2970794 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
2970814 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* *
2970835 TCGCAACGCGAATTAAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
2970856 TCGCAATGCGA
1 TCGCAATGCGA
2970867 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 27 0.45
21 33 0.55
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:2970816 original size:41 final size:41
Alignment explanation
Indices: 2970771--2970866 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
2970761 CGATTTTCCC
**
2970771 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAAGA
2970812 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAAGA
*
2970853 AAATCGCAATGCGA
1 AATTCGCAATGCGA
2970867 TACTGACTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAAGA
Found at i:2970879 original size:41 final size:41
Alignment explanation
Indices: 2970793--2970923 Score: 115
Period size: 41 Copynumber: 3.2 Consensus size: 41
2970783 GAATAAGTAA
** * * *
2970793 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTAAGAAAATCGCAATGCG-ATACTG-ACT
2970834 ATCGCAACGCGAATTAAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTAAGAAAATCGCAATGCGATACTGACT
* * * * *
2970875 ATCGCAATGCGATAATAA-AAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTAAGAAAATCGCAATGCGATACTGACT
*
2970916 TTCGCAAC
1 ATCGCAAC
2970924 ACGATACTGA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
40 4 0.05
41 67 0.89
42 4 0.05
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTAAGAAAATCGCAATGCGATACTGACT
Found at i:2970880 original size:20 final size:20
Alignment explanation
Indices: 2970855--2970949 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
2970845 AATTAAGAAA
*
2970855 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
2970875 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
2970896 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
2970916 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
2970936 TTCGCAACGCGATA
1 ATCGCAACGCGATA
2970950 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2970901 original size:21 final size:21
Alignment explanation
Indices: 2970774--2970902 Score: 97
Period size: 21 Copynumber: 6.3 Consensus size: 21
2970764 TTTTCCCAAT
*
2970774 TCGCAATGCG-AATAAGTAAA
1 TCGCAATGCGAAATAAGAAAA
* * ** *
2970794 TCGCAACGCGAATTGGGAAAT
1 TCGCAATGCGAAATAAGAAAA
*
2970815 TCGCAATGCG-AATAAGTAAA
1 TCGCAATGCGAAATAAGAAAA
* *
2970835 TCGCAACGCGAATTAAGAAAA
1 TCGCAATGCGAAATAAGAAAA
* **
2970856 TCGCAATGCG--ATACTGACTA
1 TCGCAATGCGAAATA-AGAAAA
2970876 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCGA-AATAAGAAAA
2970897 TCGCAA
1 TCGCAA
2970903 CGAGATACTT
Statistics
Matches: 80, Mismatches: 23, Indels: 11
0.70 0.20 0.10
Matches are distributed among these distances:
19 2 0.03
20 36 0.45
21 39 0.49
23 3 0.04
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAAATAAGAAAA
Found at i:2972802 original size:18 final size:18
Alignment explanation
Indices: 2972781--2972825 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2972771 TCCACTTCGG
*
2972781 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
2972799 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
2972817 GAGCCATCA
1 GAGCCATCA
2972826 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2973323 original size:20 final size:20
Alignment explanation
Indices: 2973298--2973343 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2973288 TAGTTTACTT
2973298 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * * *
2973318 TCGCAACGCGGAAATGGCTT
1 TCGCAACACGAAAATGACTA
2973338 TCGCAA
1 TCGCAA
2973344 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:2973397 original size:32 final size:32
Alignment explanation
Indices: 2973338--2973447 Score: 175
Period size: 32 Copynumber: 3.4 Consensus size: 32
2973328 GAAATGGCTT
*
2973338 TCGCAATGCGAAATGAAAATCGCAACGACAAAA
1 TCGCAACGCGAAATG-AAATCGCAACGACAAAA
* *
2973371 GCGCAACGCGAAATGAGATCGCAACGACAAAA
1 TCGCAACGCGAAATGAAATCGCAACGACAAAA
*
2973403 TCGCAACGCGAAATGAAATAGCAACGACAAAA
1 TCGCAACGCGAAATGAAATCGCAACGACAAAA
2973435 TCGCAACGCGAAA
1 TCGCAACGCGAAA
2973448 CACAAATCGC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
32 58 0.82
33 13 0.18
ACGTcount: A:0.46, C:0.24, G:0.21, T:0.09
Consensus pattern (32 bp):
TCGCAACGCGAAATGAAATCGCAACGACAAAA
Found at i:2973440 original size:14 final size:14
Alignment explanation
Indices: 2973353--2973442 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 14
2973343 ATGCGAAATG
2973353 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2973367 AAAAGCGCAACG-C
1 AAAATCGCAACGAC
2973380 GAAATGAGATCGCAACGAC
1 --AA--A-ATCGCAACGAC
*
2973399 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
2973415 ATGAAATAGCAACGAC
1 A--AAATCGCAACGAC
2973431 AAAATCGCAACG
1 AAAATCGCAACG
2973443 CGAAACACAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
13 1 0.02
14 28 0.47
15 3 0.05
16 8 0.13
17 3 0.05
18 16 0.27
19 1 0.02
ACGTcount: A:0.48, C:0.24, G:0.20, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2973476 original size:19 final size:19
Alignment explanation
Indices: 2973454--2973607 Score: 114
Period size: 19 Copynumber: 8.6 Consensus size: 19
2973444 GAAACACAAA
*
2973454 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2973473 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
2973489 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
*
2973505 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
2973521 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
2973538 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
2973557 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
2973577 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2973597 TCGTGTTGCGA
1 TCGCGTTGCGA
2973608 AAGTAAACTA
Statistics
Matches: 109, Mismatches: 15, Indels: 21
0.75 0.10 0.14
Matches are distributed among these distances:
14 19 0.17
15 3 0.03
16 6 0.06
17 2 0.02
18 14 0.13
19 36 0.33
20 29 0.27
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2973495 original size:14 final size:14
Alignment explanation
Indices: 2973476--2973533 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2973466 TTTCATTTCG
2973476 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2973490 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2973506 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2973522 CGTTGCGATTTT
1 CGTTGCGATTTT
2973534 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2973540 original size:33 final size:33
Alignment explanation
Indices: 2973459--2973549 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
2973449 ACAAATCGCA
2973459 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
2973492 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
2973524 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
2973550 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:2973568 original size:20 final size:19
Alignment explanation
Indices: 2973534--2973588 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
2973524 TTGCGATTTT
*
2973534 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2973553 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
2973573 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
2973589 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2975472 original size:14 final size:14
Alignment explanation
Indices: 2975453--2975488 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2975443 ATTGTTTAAT
2975453 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2975467 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2975481 TGATTTGT
1 TGATTTGT
2975489 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2975614 original size:14 final size:15
Alignment explanation
Indices: 2975595--2975671 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
2975585 CGAAATAGCT
2975595 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
2975609 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
2975627 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
2975646 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
2975660 ATCGCAATGCGA
1 ATCGCAA-GCGA
2975672 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:2975627 original size:19 final size:19
Alignment explanation
Indices: 2975605--2975671 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
2975595 ATCGCAACGA
2975605 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2975624 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2975642 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
2975656 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
2975672 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:2976106 original size:14 final size:14
Alignment explanation
Indices: 2976087--2976122 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2976077 ATTGTTTAAT
2976087 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2976101 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2976115 TGATTTGT
1 TGATTTGT
2976123 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2976248 original size:14 final size:15
Alignment explanation
Indices: 2976229--2976305 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
2976219 CGAAATGGCT
2976229 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
2976243 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
2976261 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
2976280 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
2976294 ATCGCAATGCGA
1 ATCGCAA-GCGA
2976306 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:2976261 original size:19 final size:19
Alignment explanation
Indices: 2976239--2976305 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
2976229 ATCGCAACGA
2976239 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2976258 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2976276 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
2976290 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
2976306 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:2976411 original size:634 final size:634
Alignment explanation
Indices: 2975203--2976543 Score: 2637
Period size: 634 Copynumber: 2.1 Consensus size: 634
2975193 TGGTAAGTCA
2975203 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
*
2975268 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTGGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
2975333 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
2975398 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
2975463 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
261 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
2975528 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACACGAAATAG
326 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACACGAAATAG
2975593 CTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGA
391 CTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGA
2975658 AAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGCGTTGC
456 AAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGCGTTGC
2975723 GATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACT
521 GATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACT
*
2975788 AATACATGCCTAACTGAAAATGTTAAAATTGCACACATAAAATACACAT
586 AATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
2975837 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
2975902 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
2975967 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
2976032 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
2976097 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
261 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
* *
2976162 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
326 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACACGAAATAG
2976227 CTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGA
391 CTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGA
2976292 AAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGCGTTGC
456 AAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGCGTTGC
2976357 GATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACT
521 GATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACT
2976422 AATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
586 AATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
*
2976471 AATGCAAGTTTTGTTAACATATATACTCCTTTTGTTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
2976536 TCAATAAT
66 TCAATAAT
2976544 AATTGTTAAA
Statistics
Matches: 702, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
634 702 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (634 bp):
AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACACGAAATAG
CTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGA
AAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGCGTTGC
GATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACT
AATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
Found at i:2977466 original size:24 final size:24
Alignment explanation
Indices: 2977410--2977468 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
2977400 AGTCAGTATT
* *
2977410 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
2977434 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
2977458 CGAATTTTGAT
1 CGAAATTTGAT
2977469 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:2977660 original size:12 final size:12
Alignment explanation
Indices: 2977643--2977679 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
2977633 ATATAATCCT
2977643 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2977655 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2977667 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2977679 G
1 G
2977680 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2979998 original size:19 final size:19
Alignment explanation
Indices: 2979976--2980073 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 19
2979966 GAAAATTACT
2979976 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2979995 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2980009 ATCGCAATGC-AGAATGAAA
1 ATCGCAATGCGA-AATGAAA
**
2980028 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
2980042 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2980061 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2980074 TTTAATTTCG
Statistics
Matches: 60, Mismatches: 7, Indels: 24
0.66 0.08 0.26
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 31 0.52
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2980018 original size:33 final size:33
Alignment explanation
Indices: 2979976--2980069 Score: 163
Period size: 33 Copynumber: 2.8 Consensus size: 33
2979966 GAAAATTACT
2979976 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2980009 ATCGCAATGC-AGAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGA-AATGAAAATCGCAACGAGAGA
2980042 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2980070 CGAATTTAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
32 1 0.02
33 56 0.97
34 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2980091 original size:19 final size:20
Alignment explanation
Indices: 2980069--2980111 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2980059 AAATCGCAAC
2980069 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
2980088 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
2980108 GCGA
1 GCGA
2980112 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:2980096 original size:14 final size:14
Alignment explanation
Indices: 2980097--2980130 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2980087 TGCGATTTTC
2980097 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
2980111 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
2980125 ATTTTC
1 ATTTTC
2980131 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Done.